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

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.