Jan Ozer (streamingmedialearningcenter.com) has updated his very helpful article on YouTube video settings over at StreamingMedia.com. He goes into great detail about overall quality, keyframe intervals, framerates, and codec recommendations. The aim is to get the best quality video after YouTube has its way with your source file (they re-encode your file, no matter what your source is).
He gives you a nice peek under the hood, with charts showing you what encoded files are created and their settings. He wraps up the article with some new recommendations — direct from the source: Colleen Henry, Video Hacker, Google Video Infrastructure.