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Flash Media Server (http://www.adobe.com/products/flashmediaserver/) is one option. There is a specific forum here on the Adobe website (http://forums.adobe.com/community/flash/flash_media_server). They'll be able to answer your questions more specifically there.
Also, a 3rd party solution is the Wowza version of FMS. Here's Wowza's comparison chart with Adobe's FMS: http://www.wowzamedia.com/comparison.html
Lastly, you can try Sorenson Squeeze Server (http://www.sorensonmedia.com/encoding-server/). I think it's one of the newer solutions, and Sorenson is a well-regarded company in terms of video compression, so at the very least you can expect the quality to be very good. Whether it's easier or harder to work with than the other two solutions...dunno...but check the user forums on the Sorenson website and see what the current users think.
Thanks for the suggestions. For the moment I am trying with ffmpeg. But sure I will need more professional tools with server side scripting.