My top 3:
1. Super Metroid (SNES)
A game that is perfect in almost every sense (it could have been a bit longer though). I wasn't really a fan of this game when it came out, but since then I've gotten to love it to bits. There's so many neat details and secrets to discover, like (SPOILER)
how you can electricute Draygon by using the grapple beam (SPOILER END). Like a fine wine, it just keeps getting better.
2. Secret of Mana (SNES)
Where to begin? There's the amazing soundtrack by Hiroki Kikuta and the fact that three people could play at the same time (this was a big deal before the interwebs, folks) and the beautiful graphics that were among the best on any 16-bit system. Best action-RPG ever.
3. Sonic the Hedgehog 2 (Megadrive or Genesis to you yankies)
I still remember the first time I played this game. I was completely awestruck, mesmorized and smitten. Sonic was everything Mario failed to be. The speed and level design was like nothing I've ever seen before. Sadly, the whole Sonic franchise has since been reduced to... well, I'm not gonna go there - too many Sonic-fanboys and -girls out there.
I gotta list the rest of my top 10 as well:
4. Street Fighter II (SNES)
5. Castlevania: Symphony of the Night (PlayStation)
6. Final Fantasy VII (PlayStation)
7. Animal Crossing: New Leaf (3DS)
8. F-Zero (SNES)
9. Resident Evil 4 (Gamecube)
10. Mega Man II (NES)