I scoured the internet looking for this answer when I built my htpc, the most popular option used to be to buy the Microsoft Media Center remote and dongle, but they discontinued it for some reason.

The best option I found is on ebay, there are lots of them. Look for the HP IR dongle with IR blaster. This dongle is affordable, can receive commands from a harmony remote configured to emulate a media center remote, and has 2 IR blaster ports and comes with a single IR blaster cable.

You can attach the IR blaster to the front of a cable box if you want to output from it to your htpc (svideo/coax analog video), and it's compatible with windows media center.