I will list a few of my favourite games, as clearly there are way to many software titles, in which a single thread could not hope contain
While the Amiga version is far better than the Atari ST version sadly there is slightly more content on the PC (DOS) version, with a intro. Still I do prefer this game on the Amiga.
Desert / Jungle Strike
There are a lot of ports of this game - some translate very well to the hand-held (some not so much) - in all truth I have probably only played a handful of conversions, however I found the Amiga version, faster, smoother with better sound and effects.
Generally better all round than the PC(DOS) version, to be fair graphically this isn't (if any) real discernible difference, but it kinda feel flat.
Unfortunate Few that are better on other systems
UFO: XCOM Enemy Uknown]
While I love the Amiga version, the PC(DOS) version of the game is better, however for musical score the PSx version has this (shame its buggy code lets it down).
While this might put the cat amongst the pigeons - the Megadrive is clearly the definitive version of this game. In fact if memory serves this is the system it was designed for. But my good friends fear not, at the end of the day the Megadrive is a cost reduced A500
Super Street Fighter II Turbo
Sorry about this but the Amiga implementations of most (if not all) fighting games is pretty dire forcing everything into 1 or 2 MBytes really screws everything up - the SNES IMHO has this one in the bag
That is all I can think of at the moment - may add more later