Some of the differences are that the 3200/3700 has twice as much memory as the 3000/3500. Also, there are a few additional sounds and some of the same sounds are mapped to different numbers. The GM sound set starts at 400 on the 3200/3700, as opposed to 300 on the 3000/3500. There is also a new version of the software specifically for the 3700 (the interface seems the same as the 3500 version, but the web site says the two are different).
Otherwise, I have found both models to be mostly the same. The main difference is the 3000/3500 is not sold retail anymore (but, yes, you can pick them up on eBay or closeout or surplus). If you buy new, you'll have to go with the 3200/3700.
Hope this helps.