Adam Sessler, of the G4 family, made some comments about placement of the left analog stick on either the XBOX360 or the PS3 last year. He said that the XBOX setup is best for when he's playing first-person shooters on the XBOX. Like the "Call of Duty" or "HALO" series. I personally like the Sony model best, since that's the one I've been most accustomed to. I just the placement is just right for me. It works best while I'm playing a GTA game, a GT game, Tourist Trophy, MegaMan Anniversary Collection, all those games. It's funny you mention the GameCube because I was playing Sonic Mega Collection on there. I'm more of an old school guy, so I appreciate having the analog stick in the position it's on the PS2 controller. I probably would forget to use the left analog stick for movement if this were the GameCube/XBOX controllers.
So I'd prefer the PS2 style since it's the easiest one for me to use and in a place I'm actually happy with. It's best for me unless you fancy something like the Nintendo 64's model.