LinkedIn Q&A : Who knows server-side software for movie fileformat transformation on ASP webserver?

I assume you need offline encoding (not on-the-fly encoding).

ffmpeg is open-source and indeed the best all-round choice, but be prepared to spend some time experimenting with command-line options, especially if you need to convert to mp4 :)

If you also need to support video formats for mobile phones, I would suggest Vidiator's Xenon encoder. It's a commercial tool.

I'm not sure what your volumes are, but if you need firepower, then you may be interested in the Ripcode appliance. Pricey, but very nice...