We've previously mentioned my favorite Apple Remote utility Remote Buddy, but the just-released RC1 adds support for the Nintendo Wiimote in addition to a variety of other supported remotes (including obviously the Apple Remote as well as offerings from Keyspan and Griffin). We've also previouslymentioned several hacks, but this is (to my knowledge) the first commercial program to support the Wiimote as a useful input device.
A while back I looked at several of the Apple remote utilities, but I finally settled on Remote Buddy as being the most flexible. It includes a variety of control sets for popular programs (e.g. iTunes, VLC, QuickTime Player), without compromising access to Front Row. Perhaps my favorite thing about Remote Buddy, however, is the keyboard and cursor emulation, which I often use to scroll on screen text when I'm leaned back and reading. Remote Buddy is shareware and runs 9.99 Euros (~$13) while in beta, but will increase to 19.99 Euros upon release (which is presumably coming soon given the release candidate). I definitely recommend it. What remote utility do you use?