Audacity audio editor , a free audio editor, just (Oct. 30th, 2006) released a 1.25 stable version that they claim supports FLAC natively. See their web page for the new FLAC supporting 1.2.5 stable release and latest 1.3.2 test version:
http://audacity.sourceforge.net/

From their 10/30/2006 release notes:

Beta version 1.3.2
Usability improvements
New selection bar
New features for label tracks
Improved toolbar docking flexibility
Menu renaming and reorganization
Selection, ruler, and playback control improvements
Major improvements to some built-in effects
New Repair effect
Improved Equalization effect
Many fixes and minor improvements to other effects
Improved accessibility for the visually impaired
Improvements for screen readers, accessibility of tracks, and hot keys
Timer recording
Auto-save and automatic crash recovery
New features and bug fixes for Nyquist
Restructured Preferences dialog
Improved batch processing
File format export improvements
Intel Mac support
Many bug fixes and stability improvements

Stable version 1.2.5
Support for new file formats, including FLAC
Fixes for Mac audio problems
Fix Generate Silence bug, a crash issue, and Linux GCC build issues
Intel Mac support

Update: I think they may want to check their FLAC support, as it shows up nowhere else in their help under File Formats supported. It will load a FLAC file (open) but doesn't show up in the pull down file type box as a supported type. A FLAC file will load but I get a distorted sounding playback. Anyone else get this to work (or not)?

Same problem here on Mac Tiger.

Problems here also with 1.2.5 on Windows XP. FLACs open (after it says ''importing MP3'') with incorrect sampling rate, channels, etc.

i just built 1.3.2 and all is well

new package at rarewares/debian in 3...2...1...


later

The current ReadMe that comes with the new 1.2.5 says that FLAC import and export support has been added but this is an error according to Audacity. 1.2.5 cannot export FLAC and may be able to import FLAC with varying results depending on the file.

1.3.2 definitely supports FLAC

it supports importing (opening) and exporting

there are some incomplete "features" with 1.3.2, tho - like the mp2 support with libtwolame is nowhere in the export options ?



later

No dice with the Mac release

Changes in Audacity 1.2.6

• Fixed memory leaks on Windows.
  
• Corrected font size problems.
  
• Enabled missing FLAC support.
  
• Fixed Mac OS X (PPC only) screen redraw issues.

i still see no ability to export, but at least it seems to open FLAC correctly now ...(win32)

I am glad I found this post. I cannot export to flac with 1.26. I'll try 1.3.2 next.

I installed Audacity 1.3.2 and as soon as I launched it, it crashed. What is the trick here? I am using windows xp, no sound card, but nivida nv mixer software for sound.