iTunes doesn't do flac. You can download flac, but need pure music or similar to convert /playback.
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If you are planning to use USB, then FLAC has the worst imact on SQ of the losless formats. AIFF is not as good as .wav, but a lot better than FLAC.
I will not argue about this. Yes, FLAC is bit-perfect when data compares are done, but it compromises SQ when played back real-time. There have been a number of studies including the one in TAS that support this.
It depends what you're going to do with it. If you send it wireless or to network Bridge/DAC then it doesn't matter (as long as playback program recognizes format). In case of Itunes+Airport Express, for instance, it is even better to keep it ALAC compressed since Itunes uses this format in transmission to Airport Express. Using AIFF would require additional processing.
Respecting the opinion of some I believe that there is no audible difference between FLAC, ALAC, WAV or AIFF. If you are using iTunes then your options, without a third party software involved, are WAV, AIFF or ALAC. When it comes to metadata my opinion is that eliminates WAV. My library is AIFF. Today I simply think there is no issue or concern with storage space and see virtually no reason for even lossless compressed files. However, looking to the future with music servers and digital players being offered by many manufacturers, FLAC may be the very best option at this time for portability and compatibility.
Steve - I understand your position. My suggestion is just that this set of article gets a lot of criticism. You may think it helps you position, but I believe it hurts your position because of all the baggage it has. You are one of the few who seems to be supporting the article. But, that is up to you.