The PS3 controller works through bluetooth on Linux, but I couldn't get it to work. I borrowed one of my friends for a while and just gave up and used it through USB. There is a thread on the Ubuntu forums that pretty much says that if it works for you, you're lucky. I looked into it a few weeks ago and it looks like it's the same. I'm sure if one person gets it working on the Pandora then it will work on every Pandora as every Pandora will be the same.
As far as comfort goes I think the Playstation controllers are perfect, that is why they haven't changed over three consoles. Perfect size for small and large hands. It's kinda sad watching a 6 year old play with a Xbox controller and someone with really large hands play a DS.
Oh yeah, I have two of the PSX controller to usb things also, that is what I use for SNES9x on both Linux and OSX. It works out of the box, and it's perfect for SNES, R1 I configure freeze state(wRite) and L1 for thaw state(Load). Mine are 1 controller to 1 USB, but they sell 2 controller to 1 USB that work with Linux. You need to check though, back when I got mine some of the 2 to 1 units didn't work. If you think the PSX or PS2 controllers are good enough/long enough cord then you should get one of those, used controllers are cheap and easy to find.