I haven't had a chance to test them all, but there are at least four applications out there including (all iTunes links): Pointer Remote (which also works with PowerPoint) ($0.99), jfControl ($3.99), AirMote ($4.99), and Stage Hand ($7.99). Three of the four require installing a small helper app on your Mac which then interfaces with the iPhone app (AirMote is the exception since it uses the Mac's built-in VNC protocols). Of these, Stage Hand seems to have the most features, including some nifty ones like advancing directly to a particular slide, on-device timers, a highlighter, and a blackout/whiteout function. (Stage Hand presently has limited Keynote '09 compatibility, but they say they're working on it.)
Let us know in the comments what your favorite iPhone / iPod touch based Keynote remote control is.