...to the AIFF vs WAV discrepancies.
First, I have read most, but not all, of the comments about this topic.
Second, I have not done the test due to the inefficiency of my current audio system.
Third, I know that on Windows Vista and 7 (and future OS's that support Windows Audio Stack protocols), if Quicktime is set to WASAPI then iTunes becomes bit-perfect. I personally use J.River Music Jukebox 12 in ASIO with ASIO4all, and foobar2k customised to use either ASIO or WASAPI (I use the latter). I also know that iTunes on Mac OS's can be bit-perfect with third-party software, or other solutions that I am not well versed in.
Fourth, if I am repeating what has been said before, I humbly beg your forgiveness.
Now, in assuming that the easy explanations of any differences are understood by all (noisy source/environment, such as HDD or thin walls; encoding/decoding converters/playback software, and so forth), and if we can imagine a very good/almost perfect playback system that exhibits almost none of said issues, I can then offer some explanations.
I use dBpoweramp Ref 14 for many things, and one unique use is its phenomenal meta tagging abilities (though iTunes is slicker in general use), and can give an immense amount of detail about an audio files properties (encoder & encoder settings, audio quality, and so on).
When I first used dBpoweramp (at the time it was ref 12), and moving away from iTunes (then it was at v8.xxx), I noticed something startling in both the Audio Properties and the metatags of many of my then Apple Lossless (ALAC) and AIFF files; there was what looked like iTunes specific audio filters added to the data!
From research, I realised what they were, and was NOT happy.
The iTunes_CDDB_ID is ok. What is not is this field:
iTunNORM
O_O
Here is some more information about what this field does
iTunes Normalization Settings
This tag will affect any file that can be meta tagged, with the exception of WAV files.
(As an interesting note, WAV audio files can be meta tagged, but not without altering, and potentially, breaking the file container, making it useless to every piece of software and hardware other than the original software that altered it).
So, although iTunes stores meta tags in both audio files and its own database, I can only say that WAV files may not be affected by this gastly tagging field, but AIFF files are.
Of course, if this field is also stored in the iTunes database as well, then I am sorry for wasting time (and I will boycott Apple until they get their act together).
I also think that ReplayGain is also used in iTunes, and that iTunes uses an internal SRC alongside Mac OS, but don’t quote me on these, as I cannot remember where I read such articles.
Finally, here are some other links about what iTunes may be doing to audio playback/audio files under the hood. As a disclaimer, most articles refer to older builds of iTunes, but these may still be relevant. I do not trust Apple on new builds of iTunes due to their history of breaking certain features between revisions/builds (and memory leakage/RAM usage) [even though I secretly still ? iTunes]:
http://www.stereophile.com/news/121707lucky/
http://www.benchmarkmedia.com/discuss/feedback/newsletter/2007/12/2/technology-update-itunes-7-windows-xp-and-mac-os-x
http://www.benchmarkmedia.com/wiki/index.php/Main_Page
http://www.benchmarkmedia.com/wiki/index.php/ITunes-QuickTime_for_Mac_-_Setup_Guide
http://designwsound.com/dwsblog/hifi-computer-faq/cas-7-itunes-pc-81110-problem/
http://designwsound.com/dwsblog/hifi-computer-faq/cas-8-itunes-pc-bit-transparent-high-resolution/
Hope this helps!
(P.S. Just FYI, I currently use EAC v1.0 Beta 2 in secure mode, with customised settings, to rip CD’s into to WAV. Then I use dBpoweramp Ref 14.2 to convert the WAV files into FLAC (v1.2.1) level 8, or LAME (v3.98.4) MP3 320 kbps CBR for special occasions. The files are then meta tagged using MusicBrainz’s Picard v0.15.1, though I also use dBpoweramp for further editing.
In my past iTunes day's, I used iTunes to rip my CD's with error tracking on, into lossy, then lossless, formats, before I seriously got into the audiophile scene ).
