Mencoder version 12 has been posted (http://babgvant.com/files/folders/misc/entry4003.aspx). Some improvements in this version are:
Changes in Version 12 are:
1) The “Stack Alignment” issues are all resolved. This will make Mencoder much more stable.
2) You now have the choice of reading the DVR-MS files with the native Mencoder demuxer, or you can read them with the ffmpeg demuxer (to use the ffmpeg demuxer use the switch –demxuer 35).
3) Slight improvement in multi-threads
4) Multiple changes in the AV sync logic to match ffmpeg a little closer.
5) A few new profiles have been added.
Some special profiles are:
1) Xvid-Archive. This profile requires you to first use ffmpeg to MUX the dvr-ms file into a mpg. Once that is compete, you can then use Mencoder to convert the video to Xvid, and just copy the audio track directly. This allows you to preserve the surround sound.
2) x264IPod. This profile allows you to use Mencoder to prepare a file for playback on the IPod. With this profile, please output to an MP4 container with Mencoder and then perform a MP4 to MP4 mux with ffmpeg.