In transcode, multiplexing is currently performed for (only) AVI files by the export modules (though there is currently (2005/1/1) discussion on the transcode-devel mailing list about redesigning transcode to separate multiplexing from encoding). If you want to create VOB files, you'll need to multiplex the video and audio streams yourself.
The tool most commonly used for multiplexing VOBs is mplex, from mjpegtools (http://mjpeg.sourceforge.net/). A typical sequence of commands is:
transcode -i source-file -o output.m2v -m output.ac3 ...
mplex -f 8 -V -o output.vob output.m2v output.ac3
Another option is tcmplex, based on bbmpeg, which is included in transcode itself; however, tcmplex has not been maintained in a long time and is likely to be removed in the near future. A slightly modified version of tcmplex is available at http://www.home.zonnet.nl/panteltje/dvd/.