Are there any advantages with the PC version except the price? Better resolutions? Is there controller support(I've seen only Xpadder will do it)?
Thanks in advance!

Higher resolutions but dreadful compatibility.
I'm really regretting I didn't get the game on Gamecube instead.
It'd be 480i and my TV is crap but at least there would be 0 graphical bugs, the pad would work native (this one is a detail, I know) and I would probably have constant 60fps.

Whats sort of graphical bugs are you talking about? I know different hardware will yeild different results but I think it was fairly flawless graphically when I played it.

With some recent hardware/drivers, BGE will produce graphical glitches (hard to describe but when you have it ingame you can't ignore it, terrible flickering) unless you set an option OFF in BGE options.
The problem is that it impacts performances. Most if not all people here seem to have found a solution and make everything work with ok performances (as some topics show), but that's not my case.
So, to qualify what I said earlier ... I think PC version is better (I generally favor PC versions over consoles) but only IF it runs flawlessly on your computer.

Thanks for the answer but I think I'll get it here with the sale :) The GCN version is harder to find too. Too bad I just bought Prince of Persia for the GCN. Oh well, I can at least connect to my GBA.

I got PoP for my gamecube too. :(
I have been really wanting to get BG&E for a while now, so I'll probably still get the $10 deal, but it would have worked out better with BG&E and Far Cry. :D
PoP is a good enough game that I don't mind buying it twice.