I use NextPVR media center.
When a recording finishes the "postprocessing.bat" is run. This allows me to set a batch script that:
-runs comskip, to create a file with all the commercial frames sequences.
-runs Mencoder, to create an AVI copy that reduces the file size to 1/8 of the original size.
-runs Mencoder, to create a second AVI copy less commercials, boost the volume by +10db and scale the resolution to my phone.
This happens for every recording. If I think I may be waiting a lot one day I'll hit sync on my phone and by the time I'm out of the shower it's loaded.
Other scheduled tasks manage the recordings, moving them about before deleting after X days.
The point is that you could use Mencoder, mcebuddy, Handbrake or any other application that has a command line interface with NPVR because of the "PostProcessing" feature.