Here are some past threads with great links to information about encoding:
http://forums.creativecow.net/readpost/20/863282
http://forums.creativecow.net/thread/20/863293#863294
If you do further google searches you can likely find even more info, although those two links provide pages of information from some of the most knowledgeable people in the insdustry. You could also do a search for onine articles by a guy named Jan Ozer, who conducts all sorts of tests on codecs and encoding software, and writes and lectures about it extensively.
But....even after reading all of that...(and I have several times over), you'll still occasionally end up having to experiment with settings depending on your source material and it's codec/format. There are literally thousands of format/codec combinations out there and each one has its own quirks, which makes it dicey to apply them globally to all video sources. Generally, the higher quality and resolution your source footage is, the better your compressed footage is going to look.
Chris Blair
Magnetic Image, Inc.
Evansville, IN
www.videomi.com
