Convert .mov to .mp4
I personally find using ffmpeg shell program (available through Brew using brew install ffmpeg) the most convenient way to do the conversions.

It includes tons of options for nearly any single thing you could possibly do with a movie.

In your case though, for a conversion, you can simply type:

ffmpeg -i /path/to/input/file /path/to/output.mp4

The .mp4 extension in the output path serves as a cue for the program to do the proper conversion -- no more options are necessary.