Apple quicktime actually does the encoding, you just have to get the Pro version. So you can get that, or use this freeware utility called Quickeditor. It'll do what you're trying to, and is shareware. I used it a while back to edit a movie trailer, so it was lying around on my hard dive. The people who make it stopped supporting it, so the file is hard to find. I was considering uploading it a server, but I did find a host.
Here it is:
http://www.amarelect.com/z-tools/Grphc/VideoEdit/
Really though, why don't you use Windows Media 9 or DivX? They're both better codecs. The WM9 encoder is freeware, but it's a bit complicated to get good results... You have to manually define the size of the movie, and the data rate for both video and audio...
If you want to try it, it's here:
http://www.microsoft.com/windows/win...m7/encoder.asp
Good luck!