Using Ubuntu 11.10 with ffmpeg and flac both installed (sudo apt-get install flac ffmpeg), I use the following transcoding setup to transcode flac to wav:
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Name ------- Convert From -------- Convert To ------- Step 1 ------- Step 2
wav>flav flac wav flac -d -c %s <None>
You probably want to avoid checking the "Enable this transcoding for all existing and new players" box or else you will screw up the webplayer (and anything else that won't support wav) until you manually change it's transcoder settings.
Then setup a new External Player (in my experience, this works best in the "with playlist" mode) and make the new wav>flac the only Active Transcoder for the player. Go back to your library, select the new External player from the player dropdown below the browsing screen, and add some tracks. This should trigger the download of a .m3u playlist file. Open this file with VLC (or experiment with other external players), and you should be good to go.
At least in 4.5... Under 4.6, I get it to play the first few seconds of each song, and then it skips to the next track. See the link in my previous post. Let me know if you can make it work.
If you run into errors, check your logs, and make sure that flac is installed and sim-linked into the Subsonic transcoders directory. If you're running Subsonic on a non-Linux machine, you may have to tweak some of the previous steps, although the concept should still work.
-Andy