With the new release of iTunes 6.0.2, Apple was kind enough to include the ability to convert your Quicktime .MOV videos to an iPod-compatible format with a few easy clicks.
I've posted a quick how-to on About.com (my home away from Lifehacker... but who am I kidding, there's no home like Lifehacker!) for converting your movies with iTunes.
How To Convert your home movies for your iPod [About.com]