What FLV encoders are available for Linux
 

I've been looking for a program to encode FLV files from MPEG, MOV, WMV etc. The only one I have found is Flix Engine.

Does anyone know of other alternatives that are out there?

That's a good question. I don't know if it will help, but the mplayer home page has many codecs and links to codecs. Maybe they can also be used for encoding.