I'm looking into developing our video content platform and part of it includes a better way for our users to upload their video content (anything from dvds, flash video, dxid, wmv, etc..) and have it automatically converted, at the moment to mp4(h.264) so that they can use it on the site though our CMS.
So what im basically asking is: What is the best CLI tool for doing this?
I use ffmpeg
It's open-source and cross platform, and used by a majority if not most of the existing encoders/converters out there.
HandBrake has a pretty powerful command line interface, documented here.
One advantage of this setup is that you can use the HandBrake GUI to configure presets and then just specify a preset name from the CLI to use that particular configuration, instead of having to specify a ton of command line arguments to configure the conversion.
MPlayer comes with a tool called MEncoder that does decoding/encoding/recoding etc of videos. Free, open source & cross platform. It's essentially very similar to the already suggested FFmpeg
