"Mastered for iTunes" at is most basic is iTunes finally opening up to hi-res masters. This means a number of things:
1) iTunes now prefers that you supply the master audio files at 96kHz/24 bit, but any sample rate that's a 24 bit file will still be considered "Mastered for iTunes." Music files that are supplied this way will have a "Mastered for iTunes" icon (like on the left) placed beside them to identify them as such.
The reason why they're asking for 96/24 is so they can both start with the highest resolution source material for a better encode, but also for a bit of future proofing in the event that iTunes later converts to a better format or a higher encode resolution (it's now 256kbs, but more on this in a second).
2) "Mastered for iTunes" doesn't mean that the mastering facility does anything special to the master except to check what it will sound like before they (or the record label) submit it to iTunes, and then check it later once again. All encoding for iTunes is still done by Apple, not by the mastering houses, record labels, or artists.
The reason for this is to keep the encodes consistent and to prevent anyone from gaming the system by hacking the encoder, but also to avoid any potential legal problems that might occur when a mastering house sends the files directly to iTunes instead of the label without their permission, or uses different specs, etc.
3) As stated above, the mastering house doesn't do any encoding directly, but Apple has provided a number of tools that they can use to hear what the final product will sound like when it's encoded. That way they can make any adjustments to the master to ensure a good encode.
One unique aspect of "Mastered for iTunes" is something that's not been publicized called a "test pressing." When Apple finally encodes the file, they'll send a copy back to the label/engineer/artist to check. If they sign off on it, the song then goes on sale in the iTunes store.
Of the few mastering houses that are currently participating in the program (all of the major ones), it was surprising that most of the time a test pressing was rejected not because of the audio quality, but because it was the wrong master. Yes, as record companies seem to do, someone would actually send the un-mastered file or a completely different song or version. Luckily, the problem is now able to be caught in the test pressing stage.
4) Speaking of the sound quality, iTunes is now using a completely new AAC encoder with a brand new algorithm and the sound quality it produces is stunning. If provides an excellent encode if you use a few common sense guidelines (more on this in a bit), and if you do, the result is almost impossible to hear (at least on the music we listened to). Certainly didn't sound anywhere near as bad as the typical MP3.
So what are the tricks to get the best sound quality from an iTunes encode? It turns out that the considerations are about the same as with MP3 encoding:
a) Turn it down a bit. A song that's flat-lined at -.1dBFS isn't going to encode as well as something with some headroom. This is because the iTunes AAC encoder outputs a tad hotter than the source, there's some intersample overs that happen at that level that aren't detected on a typical peak meter, and all DACs respond differently. Something that won't be an over on your DAC may be an over on another playback unit.
If you back it down to -.5 or even -1dB, the encode will sound a lot better and your listener probably won't be able to tell much of a difference anyway.
b) Don't squash the master too hard. Masters with some dynamic range encode better. Masters that are squeezed to within an inch of their life don't. Simple as that. Listeners like it better too.
c) Although the new encoder has a fantastic frequency response, sometimes rolling off a little of the extreme top end (16k and above) can help the encode as well.5) "Mastered for iTunes" is only an indication that a hi-res master was supplied; it's not a separate product. There will always be only one version of the song on iTunes at the same price as before. "Mastered for iTunes" doesn't mean you get to charge more, or that iTunes charges you more. Everything is like it was before, you just supply a hi-res master so it sounds better.
6) So how do you supply that hi-res master? This is where it gets a bit tricky. If you're signed to a major label, they've been contacted my their Apple reps and everything is in place, so no problem there. If you're with an indie label, insist that they contact their Apple rep for instructions.
If you use CD Baby or Tunecore, at the moment they'll tell you they don't take 24 bit or high sample rate masters. Insist that they contact their Apple rep and don't take no for an answer (this is what the Apple iTunes guy told us). Apple is greatly encouraging everyone to get with the program, so the more pressure you put on them, the quicker it will become a standard. Of course, if you can find out who your local Apple rep is (ask the local label), that could expedite things too.
The bottom line is that "Mastered for iTunes" is a great thing for digital music. As far as I can see, there's no downside to it (except maybe for the initial hassle you may go through as an indie), and you'll be giving your fans a much better sounding product as a result.