If you're talking about doing a youtube clone which converts
user video into flv's on the fly, then you should look further into the SDK tools which are offered from On2.
These allow you to integrate your own custom code with their VP6 encoder.
This opens up way more possibilities than sitting around batching videos all day yourself with any "out-of-the-box" encoder.
Check it:
http://www.on2.com/developer/