FFmpeg, is probably one of the most versatile converters around, and used in many projects across platforms.
In Ubuntu, For a quick and dirty way to convert FLV files to SWF files I use:
ffmpeg -i input.flv -acodec copy -vcodec copy output.swf
There is also a GUI-version available (cross-platform) @ http://code.google.com/p/winff/
Quite a nice post, and I've found another detailed guide on how to convert MKV to MP4 using FFmpeg here, besides, alternative to FFmpeg is mentioned in this guide.
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