For ripping, I always liked DVD Decrypter the most. Now I use the RipIt4Me / DVD Decrypter / FixVTS combo. Though DVD Decrypter is no longer developed, it is still an excellent ripper and app. RipIt4Me simply handles all the latest copy protection formats, while FixVTS cleans up the files to make them more DVD standards compliant.

Or, I will sometimes use DVDFab Decrypter to rip to the hard drive.

Then I use DVD Shrink to process the VIDEO_TS folder. Even though DVD Shrink is no longer developed, meaning it doesn't handle the latest copy protections, it is still a solid, powerful app that works very well at helping you cherry-pick what parts of the DVD you want to carry over to your backup copy. You can choose to do a full-on Re-Author if you wish and simply include the core movie and the core soundtrack and nothing else if you want, getting rid of all the menus and extras. You can also trim the lead-in and lead-out stuff, like previews and after-movie credits. Plus, you can easily preview each of the audio tracks by right-clicking on the movie playback window in the lower left of the interface and selecting which audio track to listen to. That way you can easily identify which tracks are audio commentaries and which ones are the main stereo or dolby and include only what you want.

Then you can create your VIDEO_TS folders with the final output onto the hard drive and burn that folder as a DVD Video project in Nero 6 or Nero 7. You can adjust DVD Shrink to do a deep analysis as well as "high quality adaptive error compensation" to help ensure you get the best quality you can.

One of the best things about DVD Shrink is that it is free.