-Cybernoid
That game had one good thing (on C64): the musics (That were obviously removed for the amiga version...)
Also the GFX weren't half bad, and had to be changed for the worse :-)
-Rampart
On Amiga the second player always suffered from worse controls (joystick compared to mouse) but on C64, the controls were equally bad for all (max.) 3 players (max. 2 players on Amiga version)
-Giana Sisters
Don't remember much about amiga version, but I liked it more on my C64...
-LED Storm
Not-that-bad car game on C64, but Amiga version was simply HORRIBLE (At least they could have made it scroll more than half screen at time to left and right...)
-Atomino
C64 version had fantastic musics that made very good use to synthetic sounds. Amiga version (obviously) replaced those with poor samples...