The tool you're looking for is IfoEdit. You'll also need VOBrator to peek at the vob files and see what's in each vob id (and what you want to remove). Guides on how to strip out extras can be found at http://www.doom9.org.
Basically, you'll need to rip the entire DVD to your HD, strip out unwanted extras with IfoEdit (keeping the menus), then use DVD2ONE in "Full Disc" mode to compress the remaining files down to 4.36GB.
This was the process I used to copy the Six Feet Under DVDs... stripped out the copyright warning, the HBO intro, French/Spanish audio tracks, and all subtitles. This only gave back about 300MB, but it made the DVD exactly how I wanted it, with the killer menu system and all. The resulting loss in video quality from the original was noticeable on my computer, but not at all noticeable on my 36" TV.
Stripping out extras like deleted scenes and additional audio tracks/subtitles should really help the quality of what DVD2ONE produces. I say this because I'm assuming that DVD2ONE only re-encodes the video at a lower bitrate and leaves the audio alone, giving you the most 'bang for the buck'.