The MetaFLAC tool can be used to normalize the volume of a set of FLAC files when they are played back. To achieve this, the audio data is left untouched, but a replay tag is added to the metadata.
MetaFLAC ships with the flac package, which can be installed easily:
$ sudo apt-get install flac
To add replay gain tag to FLAC files:
$ metaflac --add-replay-gain *.flac
Tried with: MetaFLAC 1.2.1 and Ubuntu 12.04