MC itself can listen for certain IR remotes. There are plugins for them available on the site (irman is one, dunno about the others).
But rather than have MC handle the remote you may want to considering using Girder instead. Sure, it's another thing to add (and buy) but it does handle 'remote-like' things in a really, really flexible manner. When you need more than just MC control you're stuck unless you use something like Girder. I use my RF remotes to send their IR (from the base station) to a usb-uirt. Girder then picks it up and sends commands to MC11, Homeseer or other apps depending on what signal was received. As in, when detecting a 'Power' key from the 'Receiver' group on the remote it tells homeseer to toggle the X10 module controlling it's AC, waits a few seconds for it to settle and then sends some IR commands to put the receiver into the 'right' modes. Not an unlikely scenario for what most folks might want to do and made possible using Girder.