Here are some of the ones that I've experienced;
1) Occasionally the phone will not connect to the data network upon boot.
Usually this is fixed by toggling airplane mode on and off.
2) Wireless tether does not work in AP mode
Had to revert to the AD Hoc apk
3) Swype will occasionally die where it can only be used in tap mode
Usually switching to the stock keyboard then back fixes that
4) G-Mail corruption
Fixed with the G-Mail apk from the EVO 2.2
5) Market not recognizing the fingerprint
Fixed by Adrynalyne by making it give a EVO 2.2 fingerprint
Other than that, I've not had any major issues. It flies - I average mid 1200s on Quadrant and consistently get 35 - 40 Mflop scores on linpack.
If you like Sense, give it a try, there are also a couple of modified ROMS by Adrynalyne:
http://androidforums.com/roms-incredible/135541-froyo-tweaked-enhanced.html
and
http://androidforums.com/roms-incredible/136054-its-peanut-butter-jelly-time-vanilla-2-2-a.html