MDRP offers an on-the-fly transcode feature which looks to be built on HandBrakeCLI.
All things considered, it's a pretty good converter: simple, slick and reliable. That said, I'm not sure how its proprietary license works with the GPL'd HandBrake underneath it.
Update 19-Apr-2012: I ended up not really bothering with transcoding my DVDs: the storage on the NAS is such that I could avoid the re-coding overhead and just rip the VOBs directly with MPlayer:
mplayer dvd://1//dev/sr0 -dumpstream -dumpfile "Some DVD Title.ps"
This way, I get all the audio and subtitle streams, and with the help of
lsdvd can pick out just the movie track (which MDRP can do as well).
One potential gotcha is to remember, particularly with subtitled/multi-audio movies, is to grab the
.INF files from the DVD, too. They contain the names of the tracks and the palette used in rendering the subs; the subs may render strangely without this information.