Since we're switching from Quicktime to HTML5 for the video player, we need to have both OGG and MP4 versions of the movie files. To convert the MOV files to OGG I installed ffmpeg2theora and then ran it via the command line to find all of the movie files in the /media directory and convert as found:

find media -name *.mov -exec ffmpeg2theora --videoquality 6 {} \;