
Encoder limitations

MEncoder - Output file must contain a video stream. Any audio-only files in the file list such as MP3 files will be skipped during encoding.

Subtitles:
FFmpeg has very little or no subtitle support. Hence you won't find any subtitle options for ffmpeg. 
MEncoder supports subtitle rendering or hard-subs. The subtitles will become a part of the video after encoding. External subtitle files are automatically loaded.
FFmpeg2theora supports soft-subs and SRT subtitles only. The subtitles will be encoded as a separate stream called a Kate stream.

Audio track selection:
FFmpeg2theora does not support audio track selection. So always the first stream is encoded.

