dependeth what platform you are on..... you may need to shell out for quicktime pro.... which will then let you export as avi.
To prevent degradation you would do well to export to the same codec - so check what codec your .mov footage is in.. and mirror it on export if poss.
Why do you want converting them? Does it bother to you that they have different file extension?
BTW, mov is a container format that can contain anything from mpeg to mp4, so why bother? Today my editing software allows freely combine avi and mov in a timeline, so what is the reason for conversion? Moreover, most of so called mov files, that you may have, are encoded with different codecs and on various quality levels, but aren't going to covert them into one "standard" codec, aren't you? I would keep them as is, unless you have some really sound reason for doing it.
Evertime I convert a MOV file to FLV the quality turns out horrible. It seems like the video plays a lot slower and is blurry. It totally loses HD quality. I went from a Kodak Zi8 which created a MOV file then converted it with two different converters and quality comes out the same on both converter softwares...
It gonna be very easy with the help of a converter software. I often use the OJOsoft to solve the problem. I saw a converter named MOV to AVI converter on its website. May be it will accomplish what u need.