Vobblanker is an excellent freeware program for editing out sections of a file.
I like to backup my DVDs mainly recorded from TV without all the menus etc, and normally use Nero recode.
If I buy commercial DVDs I like to back up the main movie only as I hate all the FBI notices (really irritating if you live in the UK!), and the extras etc, and normally the main movie will fit on a single 4.7GB disk.
I recently bought a dvd with an unusual file structure and Nero Recode, NVE, Powerproducer, DVDshrink, Smartripper, DVDdecrypter all failed to handle it (even with anydvd loaded as well).
The only thing I could do was a complete diskcopy (which meant I had all the extraneous stuff and couldn't back up to a single DVD).
I tried vobblanker and hey presto, I could edit out the bits I didn't need.
Vobblanker will work with unprotected DVDs. If you DVD is protected, either rip using one of the well known ripping programs, or else vobblanker in conjunction with AnyDVD (my normal method).
It can be downloaded from URL jsoto.posunplugged.com/vobblanker.htm
Read the guides first to understand how to use it, and then simply have a go!