I recommend this tool, because it's fast and has a lot of options for tweaking the final output.
+ It lets you encode with several codecs
+ lets you specifying the final movie size
+ visual clipping and scaling
+ normalizing audio, multiple audio languages
+ subtitle handling
- Only supports 3 container formats (Avi, Ogg, Mpeg), not Matroska f.ex.
- Audio only in mp3 or AC3, not AAC f.ex.
You should install additional software for being able to use all features:
apt-get install xvid4conf
AcidRip DVD Ripper
- Only Avi and Mpeg container
- Doesn't save your setup
- A bit confusing interface
Thoggen DVD Rip
+ Quick and easy setup of encoding
- Only supports Ogg for audio and Theora for video
- Slow encoding