As I recall, when I was thinking of doing this and performing my research, I needed to install two products:
(2) Show Analyzer
Turns out there was a whole forum devoted to "tweaking" Show Analyzer's script, to get the commercial skipping to work better. I myself felt that the commercial skipping function built into BeyondTV (which I used before Windows Media Center) was much more accurate. BeyondTV is perfectly acceptable for un-protected non-encrypted OTA recordings (e.g. through your HD Homerun), and if I hadn't added a Ceton InfiniTV cablecard tuner to my HTPC which required WMC I would probably still be using BeyondTV.
I eventually decided against wasting any computer time (or related electricity and CPU wear-and-tear) on this task under WMC. I wanted to be able to watch a recorded program either later, right after it was recorded completely, or even while it was being recorded (i.e. come in while it's still being recorded but start watching it from the beginning). These objectives were incompatible with the way post-recording ad-removal worked, not to mention the amount of time required to remove ads on hours worth of recordings.
I decided using the 30-second skip button on the WMC remote (made even more convenient through the use of a "n" number key first and then the 30-second skip, which actually accomplishes an n*30 skip with a single push) was perfectly acceptable, and far more "energy efficient".