Aside: aesthetics
Because aesthetics has such a large impact on material choices, we felt the issue needs further examination, and in particular the huge gap between what one typically see in a "natural" house and standard stick frame construction. (For typical examples of "natural" homes see "The straw bale house" by Bill and Athena Steen, or "The Natural Home" by Dan Chiras.)  Natural  houses typically have hand plastered "wavy" walls (instead of smooth sheetrock), make use of round logs or branches, and have a generally more "hand made" look.  By contrast, typical urban custom homes feature nearly flawless smooth sheetrock, the use of mostly square or highly machined wood elements, and very accurately cut woodworking, giving a more polished or machine made look.

In many ways we prefer the hand made look, especially when it includes a hint of whimsy, although we can't deny the beauty of expert woodworking.  In our minds, the hand made look creates a greater feeling of "home", and the polished look tends to say "don't touch", but without going through the actual exercise, we can't say for sure.  If we knew how to incorporate the natural building aesthetic into our urban stick framed home, we probably would have done it, in spite of how crude some of it may look to today's woodworker.  

Among urban styles, we, like many others in the environmental building community, are drawn to what is commonly referred to as the Craftsman style (not the boxy heavy timbered style of Gustav Stickley, but rather the more common style of the 1920's featuring simple, mostly angular woodworking with a sense of symmetry).  Its not obvious why this style became our internalized definition of what "home" ought to look like, other than by the process of elimination of other styles. Victorian is too ornate, Colonial, Cape Cod and Salt Box styles don't really exist in the west, the Bauhas and 1950's prairie style are too antiseptic for our taste, and the ranch and other suburban styles remind of too much of the suburbs.

But that is our style taste, and clearly an environmental house can be built in any style, and each style will have its own set of difficulties.

Material Choices

Paint - although painters may find the various non-toxic don't cover quite as well as their favorite high end paint, we find they are quite adequate and think the tradeoff is worth it.  Since we are not experts in paint chemistry and know that there are many additives to paints that don't necessarily show up as VOC's (see materials), our inclination is to go with a manufacturer that specifically aims for a low toxic product, rather than a name brand national manufacturer that has a low-VOC product.  This isn't to say that a mainstream product like Benjamin Moore's Ecospec is necessarily more toxic, it might even be lower, just that we don't know.  Since we have little info to make a  judgment, and like many other environmentally minded people, we tend to not trust big companies, we avoid choosing their products, even when they advertise heavily about how safe their product is.  If we were choosing on toxicity alone, we would have chosen locally produced Best Paint, because the people who make it are chemically sensitive and got into the business specifically to produce a low toxic paint.

In the end we chose AFM safecoat paint from the Environmental Home Center based on their experience that it was a good tradeoff between toxicity and coverage.   Unfortunately we discovered that we are not good at picking colors, and ended up hiring an interior designer to help us (humorous, but expensive story: first we tried to pick a color other than off-white, then we attempted to pick an off-white, but  it turned out to be too white to go with all the warm wood tones.  We should have painted samples of each color on a wall before painting the whole house, and just held up the construction until we got the right color).  If you're as picky as we are about color, just picking from swatches on paint color decks doesn't work well, and unfortunately all paint companies have different colors available, and the colors we ended up picking aren't any of Safecoat's standard colors.  

Clear Finish - we ended up sending most of our trim out to be finished off site.  This has the advantage of keeping the dust (and toxics) elsewhere, although we were told the finish is low toxic (its some kind of varnish).  For the little bit of clear finish we didn't send out, we've been using Daly's pro-fin, a hard drying oil that is solvent based, and so is probably toxic.  We probably should have used a water based polyurethane, but we didn't know how the durability of the two compared.  In this case we resorted to the product we've been using for years rather than research better alternatives, in spite of having complained about everyone else doing the same.

Flooring - if we were choosing on environmental principles alone, we would have used salvage flooring as much as possible, although there is not enough salvage flooring available for everyone to do this, so its clearly not the only good choice. Virtually all of the salvage flooring is Oak or Fir, and we wanted something more unusual.  We did salvage about 400SF of oak flooring from the original house, including a lot of short pieces (less than three feet) that Bob picked out the dumpster that are normally considered junk because no one will buy them, and we wanted to use as much of this as possible before purchasing anything else.

The kitchen was our biggest dilemma because we felt tile is too hard and too hard to clean, wood was too vulnerable to damage and we didn't really like the look of Marmolem that much.  In the end we chose cork from the Environmental Home Center, largely because it was on sale for half price and a number of people had told us it would hold up quite well in the kitchen due to being resilient.  We're still skeptical.  Our plan is to finish it with a water-based low voc polyurethane, even though O/S hardwax might be a better choice.  The problem is that we don't really like the dull finish of the O/S hardwax, the flooring guy charges $1/SF extra to put it on, because its expensive and difficult to work with, and we were afraid we'd have to recoat it almost every year.  If the polyurethane doesn't last, we will try to find something to patch it with, and if that fails we can always get the floor sanded and refinished with something else.  Assuming it does hold up well, it will make a wonderfully comfortable floor.

We found uses for about 300SF of the reclaimed Oak (in the guest room, hall closet, walk in closet and Bob's office), but the remainder was too small to do a whole room. Much to our surprise the flooring guys didn't mind using the short pieces at all-in fact they used them all.  Since we were looking for something different, we choose different materials for each area. For the main living area, we choose Madrone, a local wood that looks similar to cherry, and that until recently was not used due its tendency to warp.  Although FSC certified Madrone is available, (NOTE: verify with Matt at EHC) we bought the cheaper HFHC (Healty Forests, Healthy Communities- which doesn't carry the strict FSC guarantee of sustainability, but is produced by environmentally minded people who believe in the same principles) through the Environmental Home Center.

For our bedroom Kim's office, and all the second floor hallways, we picked a blend of reclaimed Australian wood that came from old wool warehouses (also from EHC).  From the point of view of transportation, its not a very environmental choice, but it's reclaimed and its mixed dark and light colors creates interest we couldn't get any other way.

For Bob's art studio, we bought OSB, screwed it down and finished it like regular flooring.

For the Guest Bathroom and Laundry areas we used Marmolem (also from EHC), and were surprised at how much we liked the look.  The other nice thing about Marmolem is that its relatively low cost.

In the master bathroom, we spoiled ourselves with a electric radiant heat mat under tile.  The heat mat draws about 300 watts when on.

In the apartment we used Marmolem throughout because of its durability.

For the two lower use stair treads, we used old bleacher boards (douglas fir) that were one inch thick, nine inches wide and sixteen feet long with eight bolt holes in them.  To make each tread, we sawed some of the material into two inch strips and then glued one strip onto each tread to get the 11" we needed.  We then plugged the bolt holes, but cutting plugs from the extra material.  Although this is a lot of work, we got the material for $2/LF and new fir stair treads are about $9.50/LF.

The main stairs is virgin oak (we didn't want to use fir, because its on the soft side-even though some people do, and we ran out of energy and time to hunt down alternatives).  The risers and skirting are all exterior grade MDF. 

Cabinets - interior grade particle board is a big producer of formaldehyde, and unfortunately most manufactured cabinets use it.  Since we were looking for cabinets that would take advantage of our small kitchen space, we decided to get them custom made.  We looked at two options: our local cabinet maker (who we know) and Neil Kelly through the Environmental Home Center.  Both make great cabinets, and both have an option to use FSC certified wood.  We did preliminary drawings, got bids from both based on them and got pretty similar prices: our local cabinet maker was about five percent cheaper.  In the end we chose the local cabinet maker because the contractor preferred having a local supplier and our experience was the he would be able to solve the design problems.  The only option we didn't pursue was finding a source for cabinets that look "handmade" (see discussion about aesthetics, above), partly because we didn't know where to look, and partly because we we'd only seen one example of the handmade look, in a cabin in rural Washington, and so didn't have enough experience to know how to design that in.

Initially we considered Madrone cabinets to go with the living area floor (and because Neil Kelly offers it as a standard FSC option), but since FSC cherry is more readily available we chose that instead.  The box is made out of FSC plywood (Europly..find out more about this).  By comparison, the Neil Kelly boxes are made of strawboard with a melamine veneer.  While strawboard would seem to be a better environmental choice than wood, we have a few unanswered questions: (1) how does it compare in sturdiness to plywood, and is the difference relevant to the longevity of the cabinets.  Does is compromise their strength in any way (2) how benign is melamine (3) is straw really a waste product, or is it only waste because the farmers use petrochemical fertilizers.

For our bathroom vanity & linen cupboard, we choose Alder, a local wood that is often underutilized.  If we had only remembered how beautiful it can be, we probably would have done the kitchen in it also because its a locally grown wood.

In the guest bathroom, we decided to get more whimsical, and bought a Mexican hand painted sink and then Bob hand made a corner vanity out of scrap reclaimed fir from the job (He calls it "reclaimed from the reclaimed") .  Since Bob is a total amateur, getting the "hand made" look comes with the territory, and so  this was the prefect place to experiment.  The countertop is also made from the reclaimed fir.  Since the vanity is relatively small (a triangle, 30" on each side along the wall), only short pieces of wood are needed, and so it was easy to find scrap pieces that had small beautiful sections.  The countertop is finished with Daly's pro-fin, a hard drying oil (but not a low toxic product!).

In the apartment, we choose cabinets from IKEA, because although their boxes are made from particle board and urea-formaldehyde glue, they modify the glue in some way so that it off-gases rapidly and so allows them to meet the European standard for Formaldehyde emissions (which is about 1/3 less than the recommended minimum set by the US EPA).  They are very low cost, of a decent quality, but the material is undoubtedly the product of some kind of industrial forest destruction.   The ones we got were made in Hungary, so they've been shipped a long way.  We also have no idea what the environmental impact at the factory is: the general consequence of global free trade seems to be that you don't get to know this things.

Countertops - we already knew there were no good choices, so we concentrated on the more durable varieties.    Granite is expensive, and Concrete and Terrazzo turn out to be in the same ballpark as Granite ($100/SF).  We briefly considered Corian, because we have it in our existing home and it works really well, but its never one of the choices listed in various "green" product lists.  We did briefly consider tile, but we really wanted a smooth, easy to clean surface, so we ended up using a product which is 94% quartz and 6% resin (presumably the same or similar to the one used in Corian)  whose brand name is Cambria (Other competitors are Silestone, Ceasarstone, and Zodiac).  Its still expensive (about $70/SF), and most of the manufacturers are far away (Cambria is made in Minnesota, but Silestone & Ceasarstone are made  outside the US),  so it fails the "locally made material" test, but we liked the look, and liked that it had only a small amount of resin.  One of our key requirement was that the kitchen a bathroom sinks be undermount, because it makes cleaning the counter so much easier, and prevents mold from growing behind the sink 

Although tile countertops can be somewhat a pain to clean, granite tile can be had quite cheaply and a very solid, good looking counter costs about $25/SF installed.  Of course the granite probably comes from Italy or Turkey or some place far away, so again it's not a great environmental choice.  The key to make tile work in wet places is sealing it well, and in our experience silicone sealer doesn't work all that well, and the number of tile showers with mold on the grout is evidence enough for us that the problem is widespread.  We certainly not experts, but it would seem that epoxy grout, or anything like it would be the only acceptable solution.  I'd be willing to use any grout if it came with a ten year warranty against mold, that didn't require you to wipe it dry all the time or reseal it every year or so.

In spite of those drawbacks, we decided to tile the ADU kitchen and bathroom counters with 12x12 granite tile that we found for about $11/SF.

In the guest bathroom the countertop is wood, and the intent had been to use a pourable epoxy resin (often used in bars and restaurants), but after asking around, that seemed like overkill, so we went with a standard clear finish.

Trim - because of the style of our house, it has a lot of board feet of trim in it.  The baseboards are 1x6, the window and door casing is all 1x4, with a 5/4 thick sill, 1x5 head casing and a 1x3 apron.  Due to the walls being nine inches thick, the sill and liners are all wide boards than normal.  The sills came from 5/4x10 stock and the liners from 1x8 stock.  Our original plan had been to use reclaimed fir (from the Environmental Home Center) in most of the rooms, and some paint grade trim in the kitchen, bathrooms, closet, laundry, Bob's studio and in the apartment, but two things conspired to make that not happen.  First was that we got FSC certified southern pine for the paint grade (also from EHC, but obviously sourced from far away, again), and it turned out to be pretty attractive stuff.  Second, we ran into the "what color" to paint it problem again, and at that point gave up and decided to put clear finish trim everywhere.  In retrospect, its not clear what we were thinking, because we like the look of almost all types of wood.

Aside from the snafu with paint grade trim, we made two decisions that together made things difficult: we decided to send the wood out for a hard, spray on clear finish (for which we're told is reasonably low toxic, and very long lasting), and we ordered the lowest grade of reclaimed fir, because Bob prefers wavy grain over the typically more expensive vertical grain.  The problem was that the reclaimed fir was loaded with "defects", and had many more knots than we expected.  While knots are perfectly acceptable in some contexts, we really didn't want the knotty pine look, so we spent a long time measuring and cutting around both the knots and areas of severe checking, and in fact most other "defects".  What we were looking for was what is often called "D" clear, but what we got was a mix over everything from top notch clear vertical gain, down to stuff that was maybe only #2 common.   Since we were sending it all out to be finished we had to identify and label every piece, cut it a little too big and the finish sand it.

This is much different from the normal process, where the trim pieces are cut and fit in order, and then sanded and finished in place.  Our process was more time consuming, because we had to identify every piece up front and either mark it or cut it once before sending it to finish (otherwise we would have sent as much as 50% too much material to the finisher), then we have to cut and fit the pieces in order to actually install them.  In retrospect, we should have either gotten the higher grade or lumber (or been more specfic about what we wanted), and maybe found a better way to do the clear finish in place.

2006 update:
In retrospect, the marking of the materials wasn't that bad and probably resulted in less waste, and a better quality end result because we chose every piece so that it would look good with the adjoining pieces. We did spend too much time patching and sanding.  Once we knew which patching compounds to use for the various size holes, we could have done all the holes in two quick passes (we did 4-5 passes on some boards).  Also instead of hand sanding, we should have just sent the whole mess out to be machine sanded.  Once we did this, then sending the whole lot out for finishing wouldn't have been a problem.  You still have to send extra to the finisher to accommodate cutting mistakes, although as far as I can the finish carpenter made virtually no mistakes.  We ended with up with enough extra to make sides & shelves for a 3'x8' bookcase.

Click here for some retrospective thoughts on materials.

Tile - tile is long lasting, and very durable, and glazed tiles are resistant to just about everything, including mold.  The problem with tile is grout, which is actually just Portland cement (and often sand), and so absorbs a lot of water, and hence grows mold.  Not only does it grow mold, but once it starts you can hardly get rid of it.  Obviously in dry places this isn't a problem, but that's not where most people put it, and its not where we want to put it. 

We considered all alternatives before decided that aesthetically, nothing looked as good as tile.  Fiberglass looks cheesy (and we fear doesn't last long), and cultured marble looks even worse.  There just aren't many choices.  The plan is to use epoxy grout to solve the problem, but we haven't gotten that far yet, and if there actually is a sealer that not only works, but doesn't need regular re-applications, we'd consider that also.  What we'd really like is a ten year warranty that says that we have to do only minimal maintenance  and that we won't get mold imbedded in the grout, or they'll replace it for free.

Miscellaneous - Kim from some old tin ceiling tiles at Second Use building materials that she is going install as wainscot in her office.  Bob found a eight panel divided light window that will serve as a re-light in the attic stairwell.  We found a pair of stained glass windows that together almost were the right size (the width was right, but the combined length is about three inches too short) for the second floor stairway window, but the project grew into a lot of work and a lot of money.  We had to hunt far and wide to get matches for the glass (the main clear glass is now discontinued and we got the next to last piece of it), then we spent hours trying to figure out how to fuse the two panels together in an integrated design.  We're still waiting to see the result.