A few resources on getting good results encoding video.
Digital Content Producer published a 2-part Basics of Encoding by Jan Ozer.
Encoding Best Practices, Part 1 Jun 9, 2008
Encoding Best Practices, Part 2 Jun 23, 2008
Great resource on Blip.tv http://blip.tv/learning/export/
From New Videographer (great step-by-step workflow)
Exporting video from Final Cut Pro and converting to Flash | News Videographer
