Hey Admiral, I use the Xbox 360 Controller - Wired. It's fantastic (when new, and hasn't suffered 4 years of Halo-use!), and makes using the Bugsier (and any other ship) even better.
If you'd like to use your wireless one's on the PC, you'll need to buy this...
http://www.xbox.com/en-US/hardware/x/xbox360wirelessgamingreceiver/ (http://www.xbox.com/en-US/hardware/x/xbox360wirelessgamingreceiver/)
I want to get that myself as I'm curious to see how my racing wheel will work with Ship Sim.