Maniac Mansion!!! for Sure! the C-64 version was way better..........the music and all. Even though the Amiga version had better (supposedly) gfx, the C-64 version played better and the sounds of footsteps when you walk are missing in the Amiga version..this was a mistake to do such a thing. The footsteps gave it character. The C=64 had less colors but the characters had....well.......more character!
Another one...........Rocket Ranger! the Amiga had much better gfx of course but again this was an amazing game on the C=64.
Also Batman The Caped Crusader (not the Movie)
and of course: Little Computer People (sigh)
there were tons of others like The Last Ninja (sigh...)
Some programmers just don't get it.........all they had to do was improve the gfx or smooth them out and add higher quality frequency to the music...........but NOT change the speed of the music and add new samples! nor change the speed or rythm at which the character moves.................they always always always screw it up!