you say they need to be compatible with USB controllers, but are these to be used with 1 pc? or do you have several computers that could each have a person with a USB controller on and be playing together over LAN?
if you mean over LAN, i can't say i know of many, but i'm pretty sure there are plenty of games that can be setup to use multiplayer over lan.
Half Life i'm pretty sure can
the old space shooter Descent could (but good luck running it on modern PCs, even 5 year old PCs are too strong)
pretty much any game that uses or comes with a server for hosting games can be setup to use a lan. this would include FarCry, Ultima Online, Neverwinter Nights 1 (possibly 2 aswell), and i'm sure other people can list many others.