This list comes down to personal preference. My personal list would look something like this:
Assassin's Creed IV: Black Flag
The pirate game everyone did not know they wanted, with a serving of Ubisoft's open world design before it became stale.
Batman: Arkham Origins
Mechanically, graphically, and plotwise (except the rival reveal) the best superhero title on the system.
Dead Rising 2
A more invested plot with combo weapons and Vegas theme for this installment of franchise.
Grand Theft Auto IV: The Complete Edition
The Ballad of Gay Tony brings the fun of Vice City back with some innovations to GTA IV's Liberty City.
Kingdoms of Amalur: Reckoning
In many ways the realization of what Fable could have been with respect to medieval fantasy.
Sonic and All-Stars Racing Transformed
The most entertaining multi-vehicle party racer with Sega's legacy on full display.
The Last of Us
A gripping zombie action game with a great plot and scenarios.
Uncharted 3: Drake's Deception
A modern action packed blockbuster reminiscent of Indiana Jones and The Last Crusade.
Virtua Fighter 5
Undisputably the best fighting game on the system with respect to mechanics and balance.
Yakuza 5
Four interwoven plots with interactive cities to explore and plenty of modern beat 'em up to go around.
* A lot of my other favorite titles had inferior ports on this system and that makes it hard to include them in this list.