I want to use a customized format to export timeline labelled "Free DVD 6mbps" specifying "mkv" extension and this line/parameters:

vcodec=theora acodec=vorbis video_rc_min_rate=0 video_bit_rate=5744000 audio_bit_rate=256000 frequency=44100 size=720x576 progressive=1

But when I export a video with this, the result is not playable with VLC/MPlayer/gxine/totem and not valid as a clip for Kdenlive project.

Which is the best solution to generate the most compatible and open video file format?

I'm not using theodora yet. for genral usability, mpeg, it's the most widly used. though quality and compression suck on it. divx is always a good genral

Ok, but I'm asking for open formats, and compatibility/usability only if it's possible.

The last versions of ffmpeg seem to support Matroska formats.