My list (whatever I can think of now)
Already mentioned:
Wizball (Smoother, and better audio on C64)
Eliminator (At least music is way better on C64)
Outrun (I think at least music was better, not sure about playability)
Atomino (C64 ingame music is SO much better...)
LED Storm (smoother scrolling + parallax on C64, way better musics... Personally I consider the C64 version the best available, better than original arcade version)
Laser Squad (almost identical otherwise (amiga has slightly improved graphics) but there are extra scenarios for C64)
Kikstart 2 (Got some vague memories about this being much worse, but can't remember exactly how)
Last Ninja series (overall better musics on C64)
