A very quick note about rotating .MOV videos shot on an iPhone 90 degrees clockwise on Ubuntu.  The first tool I tried was ffmpeg isn’t compiled with the -vf command-line option enabled. You could re-compile ffmpeg:

sudo apt-get install mencoder
mencoder -vf rotate -o Input.MOV -oac copy -ovc copy Output.MOV

(I was using -oac lavc -ovc lavc but any anonymous commenter suggested the much better idea of using copy)