Waltorious: I used a third-party USB controller and it worked fine. Fez recognized it and I was able to set controls from within the game, instead of having to program the pad myself like I have to do with most other games.
Be warned that when more recent games are made they assume you use a 360. This means button layouts can be vastly different and confusing.
Example: A PS2 for the buttons 1-4 with top right bottom left (
triangle, square, x, circle), while 360 goes bottom, left, right, top (
A, X, B, Y). Even if the game recognizes it and doesn't treat it as a Xbox controller, it may simply give you numbers (
Bard's Tale for example), and those won't always correspond with directions. And Axises could be backwards as well.
Some drivers will give you very good options for reconfiguring it to work well.