I'm making my way through FF7 again, have started Fire Emblem and Golden Sun and loving both. I'm also rage quitting my way through the various R-Type games (mostly SNES), hot damn those are hard, good fun though.
My favourite on its own would be Sonic and Knuckles, but the best, imho, is to combine Sonic 3 with Sonic & Knuckles. You used to be able to actually plug one cartridge into the other - so cool
I've been playing Car Battler Joe on GBA again recently, such a great game! It has lots of quirks but the core gameplay is solid - it's really too bad it never got a sequel. I don't know of any other games that can scratch this particular kart racer+vehicular combat+RPG itch either.
Late reply, but as someone who grew up in the era of 8-bit games, I feel like I'm still trying to catch up before I move on thoroughly to 16/32-bit. :P
Mind you, I've all kinds of things to say about 8-bit games. The stories I could tell, etc etc!