This is a tweak of part of the answer slhck gave (and thanks, slhck!) because I found that command didn't work for the latest (at this writing) ffmpeg--maybe the parameters have changed between versions?
On Windows 7, using ffmpeg v.20130103-git-9e36d9e-win64-static (decompress it with the 7zip utility), found via http://ffmpeg.zeranoe.com/builds/ in turn via http://ffmpeg.org/download.html, the following command converted a .mov file (taken from an iPhone) into a .mp4 file:
ffmpeg -i test.mov -vcodec copy -acodec copy test.mp4
I found that changing the .mp4 part of this to .avi also worked, to change it to an .avi container. With either target container, but retainusing these "-vcodec copy -acodec copy" paramaters seem to only copy the originalsource streams in itinto a new container (soin the target), so it's lossless conversion (and I'm guessing that would be the case with a variety of target containers, too).
It follows that theseThese tweaks of the batches slhck gave would work--and I've tested them and they doalso worked for me:
callConvert.bat:
for %%i IN (*.mov) DO (convert.bat "%%i")
pause
convert.bat:
IF EXIST %1.mov GOTO exit
@echo Conversion for %1 started on %DATE% %TIME%
ffmpeg -i %1 -vcodec copy -acodec copy %1.avi
:exit
@echo %1.avi already exists