I’ve had this annoyance for a while now and was too lazy to Google it. I have an iPhone docking station, an iPod docking station and my Apple MacBook. All three devices accept signals from the Apple Remote.The only device I wanted to accept signals from the remote control is my iPod since it is powering my speakers.
The solution was easier to fix than I wanted to admit. First, I switched out my iPhone dock for a Griffin Simplifi Dock for iPod and iPhone, Media Card Reader, and USB Hub in One Device (Aluminum).
Next I used this article on TUAW to disable my IR receiver on my MacBook.
Easy as Pie.