The xbox controller is basically a usb controller from the git-go. The XBCD drivers are great. So maybe that I was able to reverse either axis on either stick easily with the XBCD driver. In my experience it's pretty durable. It has more buttons, but isn't quite as comfortable. You can hack the cord to adapt to PC USB, or pick up an adapter (cable) on Ebay fairly cheap.
I like the GCN controller, and prefer it with Joy2Key for keyboard input type games (Tomb Raider, Ballance, emulators). The design of the XBCD driver setup interface, and the extra buttons swing me in favor of the Xbox controller for Aquaria though. If I could use the mouse and cursor with a joypad in Aquaria (hint hint), I'd probably use the GCN.