There are several great programs that can encode your video files into flv format. Here are a few that you can check out and see if you like.
*Telestream- Episode Engine Pro
The best in the business.
http://www.telestream.net/products/episode_series.htm
*On2 Technologies- Flix8
Great product, great prices. Works with Windows and Mac.
http://www.on2.com/products/flix/flix-pro/
*Sorenson Squeeze for Flash
Simple to use and good quality.
http://www.sorensonmedia.com/pages/?pageID=3