I haven't been able to get a controller to work in Champions Online in Ubuntu 12.04 LTS x64. When I was using Windows 7, I could use either an xinput or directinput based controller perfectly in this game.
The Controllers I have tried are:
Xbox 360 Controller for Windows (Logitech Chillstream, Via XboxDrv)
Seems to work in everything but the game itself. The in-WINE config shows everything working except the throttles.
The controllers I am going to try:
A generic USB Plug and Play controller.
(Model # COR5 E02, ASIN B00IYEZUD6)