Wii Remote, hands down. First of all, most Linux distros have out-of-the-box support for it. Second, you can connect a bunch of accessories to it, even lethal-sounding ones, such as the Nunchuk! Third, it's perfect for mouse emulation, and all you need for it to work is to put a couple of candles under your monitor. Nothing beats the Wii Remote. There's the small problem of most computer games not supporting the Wii Remote out of the box, but that's a minor issue, really.

EDIT: Almost forgot. Let's say you need a controller with a conventional layout because of a pesky game that can't be played without it. Just slap a Wii Classic or a Wii Pro controller into the Wii Remote, and bam, you got exactly what you needed.

(I'm sorry if it's a bad joke.)