Paul: If your FLACs are made from the original source, I would think twice before permanently altering them unless you plan on backing them all up first. Seems to me to kind of defeat the purpose of FLAC. That's the beauty of Replay Gain tagging--you can alter the playing gain but not the original files, and remove the tags at any time to revert playback to original, or try a different level.
Another option would be converting them all to say V0 VBR MP3's, and then you can alter the gain around all you want with Mp3gain, including permanently if you don't choose to make the "undo" tags. With those FLACs still tucked away safe and sound.