My top 5.
1) Starwing, by a long shot. The game I love so much I can overlook graphics that are outclassed by the mobile phones of about 8/9 years ago, and enjoy every second of it time and time again. I still to this day cannot absolutely guarantee that I'll make it to the end of the 3rd path. I can clear the first in my sleep, the second requires some concentration at points, the third chews me up and spits me out. A truly incredible game. 3DS rerelease please, possibly unlockable bonus in Lylat Wars 3D, I'll pay any money for them both to be on one card. Incidentally Lylat Wars is my top N64 game of all time, possibly joint first with Ocarina Of Time. Woot for 3DS rereleases.
2) Zombies Ate My Neighbours, truly hilarious co-op game that was Left4Dead before the Xbox was even a concept. Cannot get hold of the PAL version for my SNES for love nor money.
3)Jelly Boy. He can turn into a hammer. 'Nuff said. But seriously, this game's a great little platformer, well worth the 99p I paid for it on eBay for a boxed copy with manual
4) UN Squadron. True, I'm trying to dispose of my copy (again, boxed with manual) but it's still a great game. I just don't really choose it over Starwing. But it's one of the best 2D shooters ever.
5) Mario AllStars + World. Kind of a no-brainer, really. Same goes for anything with Zelda, Metroid or Final Fantasy in the title.