Materials, Sizes and Toxics
Industrialized production reduces the cost of processed materials, but results in those materials coming in only fixed sizes. Many books suggest that you should design at increments of these sizes, e.g. at multiples of 2,4 or 8 feet, but because doing so creates fairly severe design concerns, few designers have succeeded in doing this on a grand scale.
A more practical method is to design with those sizes in mind, but don't force things to them. It is more important that the building dimensions be what they need to be than you reduce the number of cutoffs you make in framing. A better solution it to keep the cutoffs in sorted piles, e.g. a piece of 2x4 that is smaller than 14½" is not useful for blocking in 16"o.c. walls, so sort a pile of shorts based on that. Someday when lumber is really expensive, you'll have to do that anyhow.
If there is one case where standard dimensions save wood, its with the 8' ceiling. Since standard construction technique for walls calls for a single bottom plate and a double top plate, the actual stud length is 92⅝" (for a framed opening of 97⅛, leaving space for flooring and sheetrock). Since the equivalent studs for both 9' ceilings and 8' with a single top plate are not nearly as common, you will likely end up chopping off a lot of small chunks--at least with 9' ceilings the chunk is just a bit over 14½", so its usable for blocking--its just that you end up with a lot of blocking.
While there is a wide variety of finish materials out there, at any given time you're limited to what is currently in style, and what appeals to a broad enough market. By seeking out antiques, and other reclaimed items, a sense of "character" is added to the building that can't be achieved any other way. These items tend to be the most loved in the house, but certainly come at a price because of the quantity of labor involved.
Natural materials/Toxics
There is no inherent reason that manufactured products have to be more toxic than less processed or "natural" ones, since some natural materials are in fact somewhat toxic. It is true that most natural materials used in construction are not toxic. The issue really isn't one of natural versus manufactured, but what the actual toxicity is. To some degree there is also a tradeoff in performance and cost versus level of toxicity allowed. Wood, glues and other natural materials will off-gas to some degree, and some manufactured materials like interior grade particle board are notorious emitters of formaldehyde. People with chemical sensitivities have a much greater concern than others.
The gray areas are the most controversial. Products like OSB, glue-lams, TGIs and other engineered wood use a glue that emits formaldehyde, but cures quite rapidly to a very low emissions level. Most green builders find these products benign, but others find them unacceptable. Since they are so prevalent, they are hard, but not necessarily impossible, to avoid.
For a public skeptical of manufactures claims, there is a serious breach of trust, and this to some degree has driven the natural building movement. By adopting a pragmatic approach to toxicity, there is very little limitation in material selection: wood trim instead of MDF, plywood and wood cabinets instead of MDF, or the occasional use of exterior-grade MDF, or one of the non-toxic MDF products.
In addition to the issue of toxicity, there is a definite "feel" created by materials. The use of "natural" materials tends to remind one of nature, while more industrial materials, such as are commonly used in the "modern" style, have a more hip, urban feel, while low cost materials are often lacking in character. While this is undoubtedly a gross generalization, I think most readers will agree that the choice of materials has a significant effect on the feel of the house, although exactly what is undoubtedly a subject of much debate.