Here's an interesting story about how non-organic soy protein isolate (commonly used in foods like vegetarian burgers) is made using a neurotoxic solvent called hexane (somewhat ironically, hexane is an organic solvent - in this case "organic" means carbon-based instead of the food production designation). The FDA does not monitor or regulate hexane levels in food.
I think it's time to stop assuming that anything made with soy protein is automatically healthy - stories like this, information about how soy monoculture is harming the environment as well as the farming industry, and questions about the biological activity of soy isoflavones (chemicals present in soy and soy products) make me think that soy is not a panacea for our health problems, but just another food that should be eaten in moderation as part of a varied diet.
Update: There have been some rumors going around that this study was funded by the Weston A. Price Foundation, a pro-meat anti-vegetarian group, but this turns out not to be the case. For an update and interesting FAQ on hexane and veggie burgers, check out More on Veggie Burgers and Neurotoxins (from Mother Jones) and also take a look at Hexane and Soyburgers: A retraction (from BoingBoing) for info on the rumors. Also, several other news sources have picked up the story.