I use mencoder which, with libdecss, can extract the files from a DVD and do a 2-pass encode. Here's a snippet from a script wot I wrote, use $INFILE as dvd://1 for example.

mencoder $INFILE $OPTS -quiet -subfont-autoscale 3 -subcp "latin1"
-font /usr/share/doc/packages/efont-serif-ttf -noodml -nosound
-vf scale=$OUT_X:$OUT_Y $ROTATE -sws 9 -ovc lavc
-lavcopts codec=mpeg4:turbo:vhq:vmax_b_frames=0:vbitrate=$VI DBR:vpass=1 -ffourcc DX50 -o $OUTFILE

mencoder $INFILE $OPTS -quiet -audio-preload 0.8 -delay 0.1
-af volnorm -srate $AUDSR -oac mp3lame
-lameopts mode=3:cbr:br=$AUDBR
-subfont-autoscale 3 -subcp "latin1"
-font /usr/share/doc/packages/efont-serif-ttf
-noodml -vf scale=$OUT_X:$OUT_Y -sws 9
-ovc lavc -lavcopts vcodec=mpeg4:vhq:vmax_b_frames=0:vbitrate=$VIDBR:v pass=2 -ffourcc DX50 -o $OUTFILE