Most of the time I export to FLV/FL4V in PP-CS4 and that works pretty well. Even so there are so many options in the preset category that I keep trying different ones. I upload to TubeMogul.com that does some transcoding and crossposting to a variety of server sites, so I don't need to worry much about the specifics.
But - I'm not really happy with the quality of the viewing on some of the sites.
Question 1 - is there a preferred/best Format/Preset for Youtube HD?
Question 2 - I've been asked to provide H.264 with .MOV container. I can't seem to find an option for .MOV output. There are several iPod output presets, but nothing that creates a .MOV file. They all create .mp4 extensions.