From a nutritional standpoint, you should think of soy in two categories: soy that is non-fermented, and soy that is fermented. The troubles I’ve documented on this site are associated with using primarily processed, non-fermented soy foods such as soy milk, flour, nuts, baby formula and the many soy products that have been flooding the market recently.
However, studies have shown traditionally fermented soy - which is the form that is wildly popular in many Asian cultures - aids in preventing and reducing a variety of diseases including certain forms of heart disease and cancers.
(More at mercola.com: Soy Bad, Soy Good: What You Must Know When Considering Soy-Based Foods)