to convert .mov to .avi:

Use the free program MediaCoder :)
But it might be kind of complicated...sorry ^^"

Or you can use ffmpeg

It comes with mediacoder, but get it alone from here: (for windows)

http://arrozcru.no-ip.org/ffmpeg_builds/bin/ffmpeg-r7760-win32.tar.gz

unpack it with WinRar in "C:\directory" for example.
(C:\directory has ffmpeg.exe)

put the video you want to convert in C:\directory (or any place you want, but with no spaces)
The video file name shouldn't have spaces too.

click start > run, and  type:
cmd /k "C:\directory\ffmpeg.exe -i C:\directory\input.mov -vcodec msmpeg4v2 -acodec mp3 C:\directory\output.avi"

and watch it encode! It worked for me. I just tried it.
it's encoded in mpeg4 and could be played in Windows media player.

see the link below for more info :)
http://ffmpeg.mplayerhq.hu/compat.html

-----------------------------
Linux Usage (By Shironeko)

FFMPEG is usally installed by default on almost every Gnu/Linux distribution.

Just open terminal and go to the directory where the video is located using the CD command. If it is in home/user/videos/ just type:

cd videos

Once in, the basic command is: ffmpeg -i inputfile.format outputfile.format
Of course you can also select bitrate and codecs, and a lot of other options. Just type ffmpeg to see all the possible options.

EXAMPLE: We are going to convert a .mov video to .avi

Simply write: ffmpeg -i video.mov video.avi

AND READY! Just watch as it encodes and in a few seconds you should be done (depending on the video length).

If you want to convert videos to OGG Theora, you should download a program called ffmpeg2theora, since the normal ffmpeg will convert your videos to OGG Vorbis (audio).

You can also use FFMPEG to convert videos to animated gifs, audio files, capture and encode live streams and a lot of things more.