I've been trying to find this out for a while. I have a digicam which produces uncompressed .MOV files which are huge. I wanted a simple way to encode those to MPEG-4 from the command line.
You have to be a rocket scientist to comprehend the command line options of ffmpeg. I finally succeded by encoding a movie using Kdenlive and eventually realized that it can export encoder scripts. Making a flexible script from such an exported script wasn't trivial for me but with some help from the mailing list of the Media Lovin' Toolkit I was able to do it.
Here's my mov2mp4 script: