I needed a quick and simple way to batch convert a set of video files using ffmpeg but couldnt find anything really simple when searching the web for an answer. Finally I managed to find a simple way using the command line tool and a BATCH for loop, heres an example:
:> for %A IN (*.MP4) DO (ffmpeg.exe -i %A converted_files/%A.avi)
In this case, your files will end up in a subfolder and be named file1.MP4.avi, file2.MP4.avi, ...). I found everything I needed to know about BATCH for loops here.