It'll be fine if you have an IR adapter installed. Anything that transmits over IR can be used as a remote control as long as you have a system for recording the codes (plenty have been written for Linux which should work under OS X) and mapping them out to commands (via AppleScript or some other scripting language as you prefer). Look into the scripts provided for Salling Clicker, etc. for inspiration. It's going to take a little work, from compiling the source for the IR detecting/mapping software, to detecting the codes, to writing the scripts, but it's a fun project if you've got the time and the willpower.
And you're not limited to the five-button Apple remote. You could also use a remote for a TV that broke, or a PDA (if you were intrepid enough to write some kind of software for the PDA to give you an interface)...anything at all.