transcode any format to *.flv - what free tool?

If I may ask, why do you need FLV? It has been more or less deprecated in favor for H.264, which Flash handles natively and is much more efficient.

You could use Handbrake to convert your videos to H.264 (in an MP4 container).

If you must use FLV, ffmpeg (free, open source) can do that. It is a command-line application in its pure form, but there are several GUI wrappers available such as ffmpegx.

 

As generic as possible:

Code:

ffmpeg -i inputfile.mov outputfile.flv

The output will probably either not look all that great, or have a huge file size. You can begin to control the bitrate of the video (b:v) and audio (b:a) like this:

Code:

ffmpeg -i inputfile.mov -b:v 400k -b:a 320k outputfile.flv

This thread contains useful information. You will also see that you can use H.264 within an FLV container, which may still work with your proprietary setup.

 

By your own admission, every user will be able to watch the video in h.264 format. However, iPhone and iPad users will not be able to watch the video if it is in .flv format.

 

Just shortly:
.flv is just a container. If the site doesn't care what's inside and you have an .mov file with an acceptable size and quality, you can just copy the streams inside and change the container to .flv. The command line for that would be

Code:

ffmpeg -i Infile.mov -acodec copy -vcodec copy Outfile.flv

Maybe that works?