Hello,
I have a camera that produces MOV videos (h264, pcm). I'd like to join all the videos to one MKV video and change it's resolution.
So far I've discovered this way how to do it which seems a little too complicated to me:
First I convert those MOVs to AVIs with ffmpeg - no re-encoding, just copy video and audio tracks. This had to be done before mencoding otherwise mencoder destroys the video (seems like it's good in joining AVIs, but not MOVs). Then I join those with mencoder to one giant AVI (still no re-encoding) and then I convert this AVI again with ffmpeg to desired MKV with x264 and vorbis.

Do you know any other "cleaner" way how to do it?
Thanks.

Well, that seems reasonable. Either way I use mencoder to join files and ffmpeg to encode them.

You can of course, do it the other way, which I would do:
1) Use ffmpeg to convert to mkv
2) Use mencoder or mkvmerge to join the results.