In addition to operating Front Row, Keynote, and iPhoto, the Apple remote is capable of a few less documented tricks. You can sleep/wake your Mac by holding down the play/pause button (particularly useful for media boxes). Pressing both the play and the menu buttons, you can also pair the remote to your machine, so that no other remote can operate it.

If you want to remote-enable your apps, there are some decent libraries available that will make this fairly painless. Martin Kahr did a great job documenting and building an Objective-C wrapper class, and RubyCocoa Resources used that to put together an example and documentation for accessing the remote within Ruby.