Here's what I do:
 Rip a dvd to the hard drive like so:
 Encode to XVid/MP# avi file:
mplayer -dvd-device /media/SOME_MOVIE -alang en dvd://1 -dumpstream -dumpfile /path/to/output.VOB
When I'm done the resulting file plays fine in Totem, but in MPlayer the audio is about 500ms out of sync. I can always just adjust the delay using the numpad +/- buttons after I open MPlayer, but it seems like it just shouldn't be this way.
mencoder -ovc xvid -xvidencopts bitrate=1024 -oac mp3lame -o /path/to/output.avi /path/to/output.VOB
It seems to only happen with some DVDs and not others though. My most recent attempt that gave me the strange AV delay had a resulting VOB file that was 5.8Gb and I'm wondering if the large file size has any effect. It also seems that in the encoding step, some files generate a large number of "Skipping frame!" lines near the start (I am wondering if this is what causes the desync). I will have to test a few more DVDs i guess to see if there is a correlation.
Anybody else have these issues with mencoder/mplayer?