I have a very old DVD which has a company logo introduction before the movie itself begins. I'd like to cut this out before I encode the movie, as it's included in the VOBs containing the movie itself. It lasts about 20 seconds.

I've tried opening the .avs file in VirtualDubMod and NanDub and trying to save only the video section containing the movie, but there's no option for me to save it as an avs file, just an avi. How can I cut out the intro and save it in a format that I can load into Gknot and encode?

When you open the VOBS in DGIndex, you can set the markers to the start/end position of the movie (move the slider on the bottom and use the [ & ] buttons to mark the start/end). Then, when you save your d2v project, it'll only save the marked segment.

vobcutter if you want to edit the vobs for any other reason, but yeah, its probably better just using DGIndex