My own personal unscientific-unblind-arbitrary-for my own amusement experiment:
Last week I went and bought the New Lamb of God album, Resolution on cd. Being a "noisy" metal album this one went into my own personal category of "not buying on itunes" So, I just went and downloaded the track "Number Six" from itunes I chose it because there is a lot going on in the song, plenty of meedley-meedley guitars, bass only moments, moments with sounds all across the spectrum from , etc. I then burned the song onto a cd. And went to my car, which has a pretty freaking solid system in it and A/B'd them.
The downloaded track does NOT have as much "punch" or "air". EDIT: It is a VERY subtle difference.
Is this scientific? No.
Do you have to believe me? No.
Is it placebo effect? Anything is possible.
Am I going to take the time to perform a scientific study and present my results to the world? No.
Will I agree that there is never any discernible difference in the mp3's you get from itunes and cd's? NOOOOOOOO.