Editing commercials with a manual video editor is crazy. How could you possibly have enough time or care enough about a single TV episode to want to do that?
There are automated solutions (discussed above) that do this with reasonable accuracy. Personally, I don't delete the commercials, I just have them marked then skip through them manually with a single button press on the remote. The accuracy is not 100% unless you spend a little time tuning it, which I don't, so you could possibly delete show content with automatic deletion of the commercials.
DVRMS toolbox can do a lot more, like transcode to other containers/codecs, if needed. It's very powerful but a little complicated.