The majority of the higher end, cross platform encodings are done using the full Sorensen 3 codec.
http://www.sorenson.com/
As for exact export settings, I don't have them in front of me, but I did actually find and download them a year or more ago. If I remember at the office I'll post them. I'm sure you could Google it and get what you want.
I believe you can process video with Sorenson either via a stand alone app (not sure, I've never done that), but certainly as a QuickTime compatible codec. QuickTime (at least QT Pro) comes with a basic version of Sorenson 3, but at a one-pass option with limited features. It'll give you a decent output, but nowhere near as good as it can get. For the best, you'll need to dump a few hundred bucks. Ouch.
I ran a bunch of tests comparing MPEG-4 to other codecs (not Sorenson 3 though). It was fairly clear to me that MPEG-4 is the best bang for the buck codec out there. It's not the best quality, but it's very decent quality at virtually all output sizes and rates. Plus, it renders very quickly on the DP Macs. And it's a true open source standard. Unfortunately, that is a meaningless statement thanks to M$. But don't get me started on that.
Of course, the side effect of MPEG-4 is that the Windows world has to have QuickTime to play them. God for bid M$ actually allow playback of standards-based media in their media player.
There is a glimmer of hope that M$ will join the world of true standards in that they submitted their WM9 HD format for standards approval. If accepted, it will be a true open source standard, meaning Apple could simply apply the WM9 HD codec in QuickTime, meaning we maintain the advantage of superior media authoring while gaining what is frankly a fantastic encoding scheme in WM9 (much as I hate to admit it).