To be honest, I don't think these "made for phpBay" sites should see any punishment in SERPs. I mean, in all honesty, I think they're pretty useful when done properly.
If someone is obviously looking for a product in niche XYZ and you really think about the different ways that products in that market can be divided/classified and you incorporate those factors in your navigation, your site truly helps consumers find what they're looking for quickly and affordably.
I don't really do any blackhat/spammy stuff and some people say phpBay stuff is in the grey area but I don't think it deserves to be. I guess the "grey" area also includes how you promote it, though.
One step further - I think more people need to think about how they can incorporate phpBay into their existing sites. Selling some related products in a little store area with a page for each category of item could be pretty profitable if your website is already getting traffick and monetized with something else.
You should be able to get pretty creative but seriously, take a look at all your existing sites and think of how you can utilize phpBay to create another stream of revenue.