Tina wants "an interior wood stain that is environmentally friendly, convenient to apply, and cost-effective." She's narrowed it down to Bioshield Aqua Resin Stain vs. TimberSoy and wants to know what we think.
Based on what we've heard from friends in the green building industry, we'd go with the TimberSoy product. A friend of ours at EcoHome Improvement tested it and was very impressed.
Initially, we thought there was an inherent advantage of TimberSoy over the Bioshield product you recommended: it looked like TimberSoy only required one coat. However, upon closer inspection, TimberSoy recommends a separate top coat sealer in either matte or gloss finish. We're not sure what exactly you're finishing, but a separate sealer coat is usually a good idea because the pigments in combination stain/finishes tend to result in a softer finish. This is especially true if you're finishing windows, doors, or bookshelves, where a sticky finish can be a real problem.
As for the chemistry involved, the two products look relatively similar to us. Both are water-based, despite the "related products" link at Green Building Products, which hawks a citrus thinner. Bioshield provides a schematic list of ingredients and is thus slightly more forthcoming than TimberSoy, which only provides a MSDS [PDF] that lists "proprietary ingredients." A base of soybeans sounds nice, but thanks to the miracle of modern chemistry, manufacturers have been able to distill "natural" things like corn and soybeans into the functional equivalent of petroleum-based chemicals. If you've followed the ethanol debate, you can imagine that soy-based finishes are not a panacea for similar reasons.
So what to do? We'd buy a small quantity of each and see which you prefer to work with, which color is better, and which finish cures more quickly. TimberSoy sells 2 oz. samples; BioShield sells a .75 liter can, but your local retailer may be willing to pour off a sample for you.