mencoder-mkv-x264.mkv

mencoder -info name=testname -oac mp3lame -of lavf -lavfopts format=mkv -o test.mkv dvd://6 -chapter 7 -hr-edl-seek -lameopts preset=standard -vf pullup,spp=4:3:0,crop=704:480:8:0,dsize=854:480 -alang ja -ofps 120000:1001 -endpos 00:01:30 -ovc x264 -x264encopts crf=20:nr=20:frameref=4:partitions=all:mixed_refs:nofast_pskip:nodct_decimate:threads=2:bframes=3:b_pyramid:direct_pred=auto:bime -o shop.mkv -msglevel mencoder=1

mencoder-mkv-xvid.mkv

mencoder -info name=testname -oac mp3lame -of lavf -lavfopts format=mkv -o test.mkv dvd://6 -chapter 7 -hr-edl-seek -lameopts preset=standard -vf pullup,spp=4:3:0,crop=704:480:8:0,dsize=854:480 -alang ja -ofps 120000:1001 -endpos 00:01:30 -ovc xvid -xvidencopts fixed_quant=3:trellis:cartoon:chroma_opt:vhq=4:max_bframes=2:autoaspect:bvhq=1:max_key_interval=300:threads=2 -o shop-xvid.mkv -msglevel mencoder=1

Both of these are stored AVI-style although their track types are "native" instead of VFW-compat. DisplaySize is set to defaults instead of the right value.