A good friend of mine Jake Hilton just posted another article on the Macromedia(Adobe) website entitled Performance-tuning Flash Media Server 2 for live webcasts using Linux. For anyone that is trying to get the best performance from Media Server this is a must read. Jake is truly an expert in this field as evidenced by his development of Huddle (a very cool web conferencing tool). He should be speaking about Flash and server technologies at conferences like FlashForward, Max, FITC, and DX3 (Lynda's new gig).
Even if you are not setting things up on Linux this is a great article that can help you understand how to optimize Media Server. Go check it out and as always,