I think a seller rating system like Ebay or Amazon would be a good idea. Not everyone knows about the BOI and Kingsnake doesn't have any sort of feedback forum because they're afraid of being sued. Alot of the crappy sellers would not still be there if you could readily see their track record or maybe they would even try a little harder.
As far as breaking down the forums further, like dividing the python forum by species, you have to have a good number of ads in each section. If you don't people just stop looking at the particular section altogether. Kingsnake, for a while, tried subdividing some of the sections like dividing the mexicana section into the subspecies, but went back because it didn't work well. The filter idea, I think, is a good one though. Would make it easy for those looking for something in particular instead of just browsing.