Using melt to join multiple files
This is a special case where I happen to have a DVD rip that wasn't detected as a single title by Handbrake. So I used melt first to join the files, then handbrake on the output.
The command to join multiple VOB files into a single (in this case DV) file. Here I'm using DV cause the source is a 4:3 video and the DV codec is very fast (though the output will be large). NB: b sets the bitrate -- without this the default quality makes the frames look very blocky.
melt /path/to/VTS_01_*.VOB -profile dv_pal -consumer avformat:movie.dv -b 5000k
After this, I use handbrake to turn the dv file into mp4 (automatically applying a de-interlace filter in the process).