Tools like mencoder, On2 Flix Engine, and GStreamer are alternatives, but they share a lot of code with ffmpeg (including the ubiquitous libavcodec).

If you want to avoid this altogether, you have a few options, though none of them are as strong as ffmpeg, like Quicktime, Microsoft (Expression Encoder etc.?), and enterprise software or hardware (Rhozet, Inlet, etc.). But I wouldn't be surprised if enterprise appliances even incorporate libavcodec today.

Yes I agree. What else could they possibly be using? And you're supposed to use it to convert videos ... what's the story?

GStreamer is another option. While support for some formats is provided in GStreamer by using ffmpeg, it has independent implementations for many formats and a very different architecture.

You can script Sorenson Squeeze through a command line but that's expensive software and was probably not available in the form that exists today when YouTube launched.

MEncoder