Every system has a stand-out title that more than stands the test of time. In order of the systems as I remember them from my collection:
Flicky on the SC3000 was obscenely hard but still a bucket of laughs, and managed to survive a Mega Drive remake and remain true to its roots.
The Oregon Trail on Mac... yeah, I know the Apple II version came sooner, but the Mac version is the one that I personally remember playing as a kid. You can still buy The Oregon Trail today to play on your modern Windows box, but don't - I tried it out a few weeks back and it's bad. Real bad. Stick to the Mac version.
The Amiga had more game titles to its name than any one person should have, most of them also ended up on the ST and various consoles too mind you. A game that's stuck with me forever though is Alien Breed, which although a little dated graphically these days still holds up on its gameplay. It survived two direct sequels (Alien Breed Tower Assault was a CD32 title even), two FPSs derived therefrom (avoid these) and a modern Xbox Live Arcade game (it's borderline...).
The Commodore 64... god, where do you start! I was playing Skate Or Die the other day while testing one of my 64s, not sure I'd call it a classic or standing the test of time though, the controls are obnoxious!
I can't tell you what was my favourite title for my Amstrad CPC, because I've never had drive belts for its floppy drive. Or any 3" floppies with anything on them...