Controllers
Real Controller w/ Adapter
The best way to emulate a console is by using the actual controller for that console. Here are some different adapters that'll let you use your controllers on your PC:
- Mayflash adapters work well and are relatively cheap.
- Bliss-Box is made to order and probably the best adapters you can buy, but they don't come cheap.
- RetroUSB, good adapters, not the best prices.
- RaphNet for Nintendo controllers.
Playstation DualShock 3
Why dualshock over X360 or FX10? Well for one thing it has the best D-pad out of the lot, but it also has: 10-bit precision analog sticks, all buttons are pressure sensitive, and can be used wirelessly with just a bluetooth adapter. You can also emulate the 360 controller, so it can play PC games natively too.
Use the new XInput Wrappers or Bluetooth Beta.
Logitech FX10 Series
The Logitech F310, F510 and F710 are all pretty good controllers. The main differences between them are that the F710 offers wireless and vibration, and the F510 just vibration, over the F310, you can compare the F710 and F310 here, the F510 is no longer being made.
If you're going down this road I'd suggest going with the F310 as it's the cheapest solution on this page at $25.
Xbox 360
The 360 controller does offer good ergonomics and many prefer it's analog stick layout over other controllers. However, it's poor D-pad means it's somewhat lackluster when it comes to emulating older consoles. I'd mainly recommend this if you've already got a 360 controller.
Note: You will need a wireless adapter to use a wireless controller on a PC.