RE4: Fair enough, I'll give it that.
Super Mario Galaxy: Now I know the hype about it, and it may be justified to a lot of people, but honestly it's not a game that really interests me as a platformer for some reason. The fact that they like screwing around with camera angles was pretty cool but I get into some situations where it's hard to see where you're going and what/when you're supposed to be dodging, and the argument that the Wii motion made it better is really hard for me to digest.
Aside from the point-and-gather-stars, I don't feel like the game would be any less worse using a GC controller.
Valkyria: Maybe, haven't played enough to really put a judgement on it
Diablo II: Back in its heyday of the early 2000s? Hell to the yes. Nowadays? I'm not so sure.
Beyond Good and Evil: Eff yeh. I was so pissed when they lied about making a sequel. ;-;
God of War II: It's God of War come on no shit
Portal: Deserves to be in the top 50, but not the top 10. A tad too insubstantial for my tastes in terms of size to compare to other puzzle-platformer type games, although it was most definitely a fuckton o fun.
Mother 3: No idea about this one
Half-Life 2: I understand the raves about it but I don't really dig it myself.
Shadow of the Colossus: I need to play this game more.
I honestly thought Gears would find at least a place near the top 50. It has a fanbase which is justifiable. (obv not the actual reason but w/e)