Windows Media Encoder is dead... In it's place is the Expression Encoder 4. There's a ton of new features, but the biggest for me is that it finally recognizes QuickTime files. If you are on a Mac, you'll need to run it under VMWare or BootCamp. But it's a free application (with a more advanced version for free).
Be sure to check it out — http://www.microsoft.com/expression/products/Encoder4_Overview.aspx
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