What is the Mastered For iTunes (MFiT) program
A long story short:
When iTunes opened in 2003, the audio files sold were 128 kbps AAC files, many of them encoded from the original CD. With the introduction of iTunes Plus in 2007, the catalog was upgraded to 256 kbps AAC (VBR).
With the Mastered For iTunes program, Apple is now accepting higher quality masters (with certain technical specifications), which they use to create the current audio encodes, and may also be used in the future to create better versions of the files sold in the iTunes Store.
Does this mean your song will sound better today? An advantage of using MFiT is that the mastering engineer can check how the master will sound when the encoding is carried out at iTunes, and act accordingly.
In addition, if the specifications of the audio files sold on iTunes do change in the future (as they probably will), Apple will already have a hi-res master of your songs to create new audio files.
Of course, this is only possible if both mixing and mastering are done using the audio files with the higher SR and bit depth available.
If you want to take advantage of the MFiT program, I will create the mix using the higher sample rate used in your recording (at no extra cost), and many of the mastering engineers I regularly work with offer MFiT masters (some at an extra fee, please ask).