How do you convert an entire directory/folder with ffmpeg via command line or with a batch script?
Getting a bit like code golf here, but since nearly all the answers so far are bash (barring one lonely cmd one), here's a windows cross-platform command that uses powershell (because awesome):
ls *.avi|%{ ffmpeg -i $_ $_.name.replace($_.extension, ".mp4")}
You can change *.avi to whatever matches your source footage.