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i'd suggest the 360 controller, due to the fact that you can just plug and play. i haven't tried using a ps3 controller with my computer in a while, but i remember the setup being a ***** for whatever reason. i guess it would come down to how important the dpad is to you. if you plan on playing fighting games then the ps3 might work a little better, but that's if you're okay with going through the trouble to set one up. though the convenience of the 360 is just too hard to beat. i'd stomach its horrid dpad solely for that reason.
I would suggest an Xbox 360 controller, wired or wireless.
I've used a wireless for years now, receiver work flawlessly, the recharable battery pack still holds a full charge (lasts about a month or so before needing charged), and the native support is always a good sign.