The simplest program that can do this is DVD Shrink. You can select to take out perhaps unwanted commentary, or other unwanted audio streams.
I collect untouched DVD’s to my hard drive. Sometimes I would like to cut some extra stuff (like credits) out of the stream. Now, I need to do this without re-encoding the WHOLE thing to minimize quality loss. And I also need to fade in/out the audio. Can anyone point me to this kind of software? I’ve been searching the net for ages, but there doesn’t seem to be an editor that supports .vob files. :(