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[drewzor]

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[Jack&Water]

I'm pretty sure you're going to have to do this manually. If you're capturing to divx, use Virtualdub to cut out the commercials. If you're capturing to mpeg, check out one of the products from Womble like MPEG Video Wizard or MPEG VCR.

[drewzor]

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[jagabo]

In VirtualDub use mark-in and mark-out to mark each ad segment, then Edit -> Delete Section. Repeat for each ad segment.

[Jack&Water]

Vdubmod should work fine, so long as the files are of the same frame rate and bitrate. Otherwise you'll have to re-encode.

For making cuts with Vdubmod, use the two arrow buttons to mark in and mark out the section of your vid. If you want to save that selection, just go to "file>save as" and select an AVI container. If you want to remove that particular selection of your vid instead, just hit the delete button, or "Edit>Delete". Make sure you have "Direct Stream Copy" selected in the video menu for either task before you save. One more thing, know that you can only make a cut on a key frame. Make sure that you are using the two key buttons to navigate your video when making edits.

If you want to join files, open your first video, then go to "File>Append Segment". Again, make sure you select "Direct Stream Copy" before you save.

[reboot]

You can do this automatically, depending on the software.
Get comskip and comclean, then run them from your pvr software postprocessing, or use dirmon to run them.
You could also use comskip and videoredo.
If you want further details on how this works, check the gbpvr forums. Comskip is not specific to gbpvr, and can be used with just about any capture card and pvr software (with dirmon).
It's all free (except videoredo of course).