FLAC support is available in some builds of Sonic Visualiser; I'll try to look into extending support for it in future builds.
Whether FLAC support is available or not depends on whether it was included in the build of libsndfile that Sonic Visualiser was linked against (libsndfile is capable of reading FLAC files, but only if the FLAC libraries have been compiled in to it).
The Linux builds of Sonic Visualiser 1.5 _do_ have FLAC support included in their versions of libsndfile, and should be able to open .flac files directly (davidf, do you not find this to be the case?).
OS/X and Windows builds currently lack FLAC support.
Sonic Visualiser on OS/X is actually capable of opening any file supported by QuickTime, so users on OS/X might be able to get it to work by installing additional QuickTime codecs (I don't actually know offhand whether there is one for FLAC, but it seems likely). One limitation here -- this is a bug in SV -- is that any file types supported by non-core QuickTime codecs will not be automatically enabled in the open-file dialog: you have to set the file dialog to "All files" rather than "Audio files" before it will let you select one of them.