People who play CoD don't give a shit about what PS3's defining game is. To them it's either CoD or Madden. This kind of question is only relevant to enthusiasts and games like CoD and Madden are beyond them. It's not really a question of quality for those games, they just aren't "special". Hell I'd say CoD4 is beyond console defining and just Gen defining. What games are the enthusiasts going to look back at and in a "Best PS3 game thread" going to post?
It's going to be stuff like Uncharted, Metal Gear Solid, Valkyria Chronicles, Demon Souls, ect ect.
It's pretty obvious that Uncharted 2 is the most obvious answer. I mean you core gamers loved it, it displayed how awesome PS3 games looked, and seems to be a leader and inspiration in the "lets make games real cinematic" trend. Hell, as far as I can remember, it seemed to be the real beginning of "man PS3 has some awesome exclusives" thinking.
Other then that, maybe MGS4. It was a big deal exclusive. I mean I think it's terrible, but a lot of people out there really seem to love it.