I had an issue pairing my Apple Remote with my MacBook Pro. The Apple manual says (on page 36):

To pair your Apple Remote with your MacBook Pro:

1. Position the Apple Remote 3 to 4 inches from the IR receiver on your MacBook Pro.
2. Press and hold the Menu and Next/Fast-forward buttons on the Apple Remote for 5 seconds.

After trying and failing several times to pair my remote using these instructions, I gave up. While it could be a bit annoying not to have the remote paired, it was not a significant enough issue to prompt me to send the notebook in for repair. After a few days, I decided that there must be a software conflict causing this problem, since the remote works fine otherwise. I scoured the net for a solution and found nothing. It seemed I was the only one with this problem.

Based on the premise that you should push all of the buttons and see what happens, I tried several other key combinations on the remote. To my surprise, holding the Menu + Play/Pause buttons together for five seconds paired the remote with my MacBook Pro.

I have unpaired and then re-paired the remote several times with this alternate button combination and it works every time.

[robg adds: The Intel mini instruction book reads the same way, but those keys do work to pair the remote on the mini (the Play/Pause button also works).]