A crapload of Mega Man games- After years of dabbling in the various Mega Man games and then giving up because of their difficulty, I finally happened upon "easy scenario" in the Mega Man Zero Collection for DS (yeah, I know, I'm a wimp). I played through it and loved the gameplay and story, prompting me to play through all the Mega Man games, but on the regular difficulty. I plowed through Mega Man X and X2 on 100%, finally muscled my way through Mega Man Zero 1 on normal difficulty (I swear, that too WAYYYYYYYYY too long), and picked up a PSP 3000 just so I could play Mega Man: Maverick Hunter X (also 100%, normal difficulty). Right now, I'm working on an original Mega Man run and a Mega Man ZX run, and I'm really liking both. The only sour taste I've had thus far is Mega Man X8... ugh, I gave up after 20 minutes, the controls were clunky, and the tutorials were so not-Mega Man.
Cave Story- My first experience with this game was the 3DS eShop version that came out this year, but since it's just a port, I'm not counting it for the 2012 games. I don't know how I passed this game over so many times. It's like a love letter to every old game I like.
Sonic Generations- I actually haven't played a Sonic game since Shadow the Hedgehog which, unlike most, I actually liked. But I heard all the terrible things about Sonic 06 and Unleashed, so I didn't have many hopes. The fact that I consider the Adventure titles to be terrible games (despite liking them) didn't really help. But when I picked up Generations, I was thoroughly surprised. For the first time, 3D Sonic felt fast and smooth, the way he's supposed to be. Easily the best Sonic game I've ever played.
Metroid Prime Trilogy- What happens when you take a pair of archaic, single-stick shooters, and give them motion aiming? They become really fun shooters on the cutting edge. Who knew?
Super Mario Galaxy- I was expecting another good 3D Mario game when I picked this up, but I wasn't expecting it to be this freaking GOOD.
Kirby's Return to Dream Land- Laugh all you want, I think this game is LOADS better than NSMBWii, despite being a bit too easy for the first few worlds. The music, gameplay, multiplayer, music, and even finall boss battle were all amazing (something I often find myself disappointed with in more modern games).
The Legend of Zelda: Ocarina of Time 3D- The first Zelda game I played, remastered with better visuals, 3D effect, better frame rate, smoother controls, and new play options taking advantage of the 3DS's special features? Sign me up! The fact that it includes Master Quest and a boss rush mode helps, too. This is the definitive version of a classic, which doesn't happen too often with remakes.