Can I use an Apple remote to control a keynote presentation?
Yes - although most people are using the iOS based Keynote Remote these days, the old infrared (which is very thin / physically touchable and very reliable in dark rooms and easily hidden in a hand) works just fine.

The Keynote '09 help shows what functions the various buttons will perform when you are in the various modes: Keynote window itself, presentation mode and slide switcher mode.