Looking at the avconv website there seem to be a vast array of options to convert video.
However, I'm getting lost in all the technical detail.
Is there a simple way to convert a .mov to a .mp4 (or h264)?
I'm happy if it's slightly lossy.
If it helps I'm on Ubuntu 12.04.2 LTS.
In a very basic form, it would look a bit like this:
avconv -i inputfile.mov -c:v libx264 outputfile.mp4
This will only work if you compiled avconv with libx264 support - you can see here on how to do that.
avconv -i inputfile.mov -c copy outputfile.mp4
This will copy all codec information from the .mov container and place it into the .mp4 container file.
Just as a note, avconv is a fork of ffmpeg, many of the switches for ffmpeg will work for avconv (if that helps your search for answers)