Okay I'm sensing this is now is the time to open up this discussion a bit so I've moved the thread to the main 'Movie Copy Software' forum.
In general here's what I do with DVDs.
This isn't necessarily right for everyone but it's what I find gives me maximum flexibility with regard to customising the disc and maximising quality (which is one of my own key priorities).
1). Rip full disc with DVDFab.
2). Open the disc in PGCEdit.
3). Run the 'Remove Useless Stuff' function which executes a whole suite of functions that get rid of unplayable content, dummy titlesets, remove unnecessary commands etc. and essentially simplifies the structure of the disc.
4). If required, use the 'Jump to PGC' function to bypass unwanted stuff at the start of the disc.
5). Kill playback of and blank all unwanted titlesets (extras, warnings etc.). This can be done on an individual basis so it effectively allows you to include exactly what you want.
6). Edit the menu buttons to remove links to deleted content.
7). Run the 'Remove Useless Stuff' function again to remove any additional content that is now no longer playable.
8). Use the FixVTS option to recover the space occupied by the deleted content and save the disc before closing PgcEdit.
9). If the disc requires compression I'll run it through DVD Rebuilder for maximum quality. If it doesn't require compression then I go to to straight to step 10.
10). Burn the disc.
There are other tricks that come into play if you want to avoid compression or maximise the space for compression which optimises the quality.
Menushrink is a good way of recovering additional space and converts motion menus to stills.
Sometimes it's also possible to completely remove unwanted titlesets by editing the calling commands and re-running the 'Remove Useless Stuff' function in PgcEdit but you're starting to get into the really technical stuff here regarding DVD command structures.