I use Front Row on my iMac a lot, and my iPod is docked next to it.
Annoyingly, it keeps turning the iPod on and playing music when I use the Apple Remote.
Any ways to stop it other than just covering the IR sensor?
Sure. Funny you should ask, I JUST looked this up because I bought a new dock today! Anyway...
Pair one of your remotes with just the iMac. Get real close to the black Apple logo on the front of your imac (like 3 inches close) and hold down "Menu" and "Fwd" together for more than 5 seconds.
You should get a chain-link icon flash up on screen. Now your remote will operate only the iMac.
Now, for fun, let's set the DOCK to only work with the one remote:
Dock your iPod, and turn it on (Do this away from your iMac if you can). Get the other remote real close to the dock and do the "Menu" & "Fwd" press + hold again for 5+ seconds.
Now that remote will control the dock only.