There are a few options for using remote controls other than the Apple remote on the Mac. The one I have explored so far is through the Remote Buddy software. It supports quite a few remote controls, including certain IR receivers that also work with Windows Media Center - but not all of them. I advise that you try the 30 days demo version of it to test if your hardware is supported or not.
There are various small details to consider using this. Not all remotes can wake up the computer from sleep for instance. So far I've been using a PS 3 Bluetooth remote with it. While this works great and has a ton of buttons to configure to your liking, you need to set the software to automatically disconnect the remote after a short delay else you'll find yourself replacing the batteries in the PS 3 remote everyday. The disconnection means that the next remote key press will trigger a reconnection, which takes a few seconds to happen and thus need some getting used to.
I'm going to try soon using the Apple built-in IR receiver with an Harmony remote; there is apparently a Plex remote profile on the harmony that mimics several apple remotes to allow more than the default 6 or 7 buttons limit on a single apple remote. I'll try to make this work with remote buddy & eyeTv. Normally this would allow waking up the computer and would not have the disconnect / reconnect latency inherent to using the PS3 remote (when you want a decent battery life).