I have it for Wii; the guitar is a bit heavier (which you may or may not prefer) due to the Wii remote inside, the strum bar is a bit "clickier" (which again you may or may not prefer) and maybe louder when you press it.
The tilt sensor is a bit more sensitive (which I personally like, though during the really, really hard songs I've set it off accidentally when I was slamming the buttons down hard and rocking out).
The Wii version also has rumble (which you again may or may not prefer, but it can be turned off), and you hear mistakes coming from within the guitar rather than the screen.
The 360 has better graphics (who cares on a game like this?) in the background, and a better player-matching system for online play (XBox Live).
2nyriggz has the 360 version...I'm curious to hear what he has to say.