I have some old logitech wired dual shock clone (treated me pretty well), a ps3 controller (i have a ps3) and a wireless 360 controller. If i was inclined to play emulated games that i owned, I would use the 360 controller. I do plan to eventually get a bluetooth adapter to try out the ps3 controller though.
It has been a while since i looked in to it, but if you use the official drivers for the gamepad, there is no difference between wired/wireless 360 controller. Well, other than how the wireless 360 controller COMPLETELY EATS BATTERIES. The difference comes in that the wired supports using significantly better 3rd party drivers which offer much greater customization, support and features. At the time i looked in to this, the wireless 360 controller did not support them. Wireless also cost more when i bought mine.
360 controller has in my experience the best plug and play support on pc. Games just support it easily generally and in game icons for controls generally are for the 360 controller.
the ps3 controller supposedly works very well with a 3rd party driver, but i haven't tried to get mine to work on my pc (no bluetooth adapter). However, i don't see a reason to pick ps3 controller over 360 given how no game is going to directly support ps3 controller as anything but a generic gamepad (not a terrible thing of course).
If you just like the ps3 controller better or are playing playstation 1 emulated games on your pc, go with ps3 gamepad. All other situations go with 360 WIRED gamepad. if you insist on going 360 wireless, make damn sure you buy the thing that lets you recharge it via the usb.