Did the OP get -1 rep because he had Call of Duty: Modern Warfare 3 on there? You anti-CoD fanboys are hopeless.
Anyway my top 3 were
1. Persona 3 (also my favorite game ever)
2. Final Fantasy VII (over 15 years old but I didn't play it until 2012)
3. Devil Survivor
Does it have to have been released in 2012 as well?
If not then it's probably Red Orchestra 2: Heroes of Stalingrad for me.
The Witcher 2: Enhanced Edition was released in 2012, but it was a remaster of sorts so I don't know if that counts.
I'm really picky when it comes to games, there are few I've played that I would be proud to call good (doesn't stop me from nerding all the "average ones" however)