A couple people have mentioned how they have either stopped eating soy or were concerned about eating soy after reading some of the reports that have come out over the last few years.
These reports claim that there were several health hazards associated with eating non-fermented soy products. Examples of non-fermented soy products are soy milk and tofu while examples of fermented soy products are soy sauce and tempeh.
In addition to the increased breast cancer claims, I have also seen information (see above article) of the dangers of feeding too many soy-based products to children due to the amount of estrogen in these foods. This is a particular concern for growing boys and I'm sure, according to the claims, there are issues for girls as well (pre-pubescence being one).
I did a little poking around at some of these reports. It seems that one of the most quoted articles and books was written by a woman who is a huge proponent of raw milk products. Her PhD is from a distance learning program and is non-nutritionally related. Now, that's not to say that her claims do not have merit. Many of the other articles point out how non-fermented products contain "anti-nutrients". I haven't found any good sources about what this actually means, but it is always considered with a nefarious tone.
Now, I am no research scientist, nor have I spent a great deal of time analyzing the different reports and have yet to find anything concrete in a medical journal, but I do think there is some merit in the issues with soy processing. For example, the chemicals used to process soy into soymilk sound like bad customers. There is also the issue with genetically modified soy or non-organically grown soy products. Not to mention the fact that soy, in some format or other, shows up in a considerable number of processed foods (snack foods, protein products and the like).
So, suffice it to say, I think that if you consume reasonable (read: small) amounts of soy milk and tofu that is either made yourself or without the massive processing you are probably safe. This is more in accordance with traditional Chinese and Japanese diets. In other words, the diets that generally get all the high marks for health and longevity -- the ones that include fermented soy products like tempeh and soy sauce with some modest amounts of tofu and soy milk and lots of green tea.
If you are truly concerned with the health risks raised by soy, then I would encourage you to do some of your own research. If what you find bothers you but you are not ready or willing to give up soy products, then perhaps switch to an organic soy product and/or think about making it yourself.
As for me, I don't consume a tremendous amount of soy - maybe a couple cups of soymilk a week and tofu or okara on occasion and I make it all from organic soybeans. My kids still drink organic cow's milk. I'm sure we still ingest more soy by-products than we know and it's something I may be more cautious of, but it's not something at this point that I'm going to avoid. Who knows, non-fermented soy products may turn out to be the next witch hunt like trans-fats.
In the meantime, keep an eye open for new studies and results. As we all know, health food claims or warnings can change with the tides as new research is done.