Hello,
i want to know which are the best for converting videos FFMPEG or Mencoder?

in output quality, in fast conversion, in output size, in server friendly, also for H.264 output.

Thank You

No big difference. We used to use mencoder.

All depends what is your encoding command. And there is no one perfect command.
In case of x264 files - final output file is always mp4 file.

What we do:
First mencoder converts raw video (2 passes) into x264 log and temporary x264 video file.
Next mplayer extracts raw audio to wav file
Next wav file is converted to mp4 audio (acc format)
Next temp x264 is merged into m4v file
Next mp4 audio is muxed with m4v file
Next meta info is generated
Finally m4v video file is renamed to "mp4" or "flv"
All temporary files are deleted.

Final extension is not important (mp4 or flv). Container is always mp4.

But before all these conversion commands execution we do complicated calculations based on original video details and properties to generate best posible mencoder command.
Without it you have small chance to write good and working mencoder command.

D.