iTunes

To obtain bit perfect playback;

Disable all DSP like "Crossfade songs", "Sound Enhancer" and "Sound Check"

Disable the equalizer

If you use an outboard DAC over Toslink or USB; set volume to max

In Audio MIDI Setup match the sample rate with the sample rate of the audio.

iTunes uses a fixed sample rate.

Audio with a different sample rate is re-sampled to the setting in this panel.

If you want automatic sample rate switching you need a third party product like Bitperfect.

Source: krmathis

FLAC

Just like Microsoft, Apple don’t support FLAC.
You can install Fluke to import FLAC in iTunes.

You can use software provided by Xiph.

A detailed description can be found here.