For me it's:
STALKER Series - Weapons are basically reversed and everythings on the wrong side, this annoys me even more with the SA80 as everything would be pointless on the other side of the weapon (Unless its one of them specially designed 'leftie' ones that dont actually get used)
Homefront - The occasional jerky animation. This happens in just about every game out there, but I notice it more in this game.
Saints Row 2 - Clothing clipping through other items of clothing. This usually means that cool guy look you perfected is ruined.