I think it was a while back that I updated my itunes and it started doing this, it has really been pissing me off lately and I was wondering if there was a way where you could go into a game with lower resolution than your desktop and not fuck windows up... seriously everytime I come back from a starcraft game itunes its really ugly and 640x480 and all that. Like I said it all started after some shitty itunes update.

It should automatically resize your desktop, and you should be able to press the maximize button and it should go back to normal. If that doesn't work, there's probably nothing you can do other than restart it. Or use winamp or something.

That's because StarCraft uses old methods of changing resolution. I notice it even on SEN sometimes when pictures are 256 colors only.
There's probably not much you can do about it other than using chaos launcher or something to play it windowed.