Seconding any Logitech USB controller that's vaguely Xbox-ish. I used the basic Logitech F310, and it's great.
The Retropie setup pretty much assumes you're going to use an F310 or similar, so using anything else is hard. It also helps to have a keyboard on hand, as some systems can get very keyboardy.
‘Remember the Golden Rule of Selling: “Do not resort to violence.”’ — McGlashan.