There are programs available to do this:

Dvredit, Dvrms editor and Dcut are freeware - commercials need to be removed manually with these programs. Dcut let's you cut commercials while sitting in front of your tv set, by using your MCE remore control.

VideoRedo 2.2 is commercial software however you can download a trial of this version from http://www.hyperreality.com.au.