This will allow you to play .flac with iTunes.
It does, however, assume you know how to use a command line prompt.
For Ubuntu
sudo apt-get install ffmpeg
For OS X
brew install ffmpeg
For both
Navigate to the directory in your terminal of choice.
for f in *.flac; do ffmpeg -i "$f" -acodec alac "${f%.flac}.m4a"; done
All credit goes to this Audio-Video Production StackExchange answer.