Any more than a few videos in number and I would highly recommend mencoder. It is complicated to get a command line string that is right for you, but once you do, you can't beat it. I use it to get some sanity from the awful QT files that my cheapy hd camera produces.
I have a script which finds them on the flash and can dump out virtually any format (and size) by only changing one line of the script.
The reason I mention all this is because of my quicktime files must be decoded with mencoder first as most of the gui programs cannot interpret this weird format without either crashing or losing sync.