We use and recommend Sorenson Squeeze everyday. The Flash VP6 codec is great and will give you great video quality at small file sizes. With Squeeze you can set up batches or watch folders that will take incoming AVI files and automatically encode to SWF/FLV. When it's done you can have Squeeze automatically FTP it to your site.
Next version of Flash Player will support H.264 video + AAC audio!
You can get the beta now at labs.adobe.com
Just announced and released (the beta) today.
Works like a chizzzarm!
Anyhow, Adobe's encoder is limiting because it can only do 1-pass. On2's Flix can do two pass. I cross between both as necessary (as Adobe's interface is much simpler), but for our workhorse encoding system, we use Flix Engine on Linux.
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