Incidently HandBrakeCLI works pretty well. For some reason Handbrake 0.9.1 for Windows couldn't rip a track from one of my Monk DVDs. Threw it in my linux system and it worked fine with these settings:
beeblequix@mylinuxbox:~$ ./HandBrakeCLI -t 2 -m -e x264 -b 1500 -r 23.976 -2 -d 1:1 -7 -8 -E aac -B 128 -R 48 -i /media/cdrom/VIDEO_TS/ -o ~/Movies/Monk.s5.d1.e2.m4v
This link was invaluable in understanding how to enter the different settings. Too bad there's no GUI for linux yet because even though CLI is pretty powerful I think it's just as powerful with the GUI on Windows. Wonder if a frontend for it could be made with Qt3 or ncurses?