So, here's how I fixed it on my server, which is running Ubuntu 10.04, but this should work on any Ubuntu system certainly, likely any Debian system, and substituting the package manager commands for appropriate ones, likely any other Linux system as well.
This requires the "multiverse" repositories to be enabled on Ubuntu (in my case, lucid/multiverse, lucid-updates/multiverse and lucid-security/multiverse)
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sudo apt-get install ffmpeg libavcodec-extra-52 libavdevice-extra-52 libavfilter-extra-0 libavformat-extra-52 libavutil-extra-49 libpostproc-extra-51 libswscale-extra-0
now either remove or rename the shipped ffmpeg package:
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sudo mv /var/subsonic/transcode/ffmpeg /var/subsonic/transcode/ffmpeg-bak
and symlink in the system one:
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sudo ln -s `which ffmpeg` /var/subsonic/transcode/ffmpeg
and you're done!