I believe Hasbro is rereleasing the shows on to DVD at some point either this year or next. They just started releasing Transformers on DVD (I believe in cheaper thinkpaks seasons) through a third party, and said they'd do MLP too.
Just a bit of history: Rhino Video at one point held the licenses to TF, GI Joe, MLP, and Jem.
MLP was at first released on a dvd set, and I found it very disappointing with the cover art they chose (although they may not have had the rights to any others at that point), and the fact that they put the cut-up tv versions of the specials, cutting out one song each "A Little Piece of Rainbow", and "Good Old Days" respectively. Then Paramount stormed in (about the time the TF movie hit theaters, good job Paramount!), took at least the TF license away from them, GI Joe and Jem disappeared off the radar almost immediately after that, and MLP limped toward some kind of conclusion with single discs for the rest of the 80's show from Rhino. MLP Tales (the 90's series) never made it to DVD with them, and that may be because they lost the MLP license, or they never had it to begin with for Tales. MLP Tales was released on DVD in the UK, and there was a short-lived G2 cartoon in the UK, which I have only seen cover art for tapes of, but never actually watched (and I'd kill to see, personally!)
Hasbro has since taken back their ENTIRE animated library (Go Hasbro!) and has negotiated with a third-party dvd company to release the old shows on DVD. I HOPE this means Glo-Worms, Moondreamers and any other little known shows from them see the light of day again, as well as GI Joe, Jem, My Little Pony return. Transformers is already out on DVD again, due to the hype of the movies. I assume GI Joe will be next.
(Wow, so much info you didn't need to know!)
As for Itunes, one can dream, but I don't see that happening. I could see their library MAYBE on Hulu, Joost, or Youtube, where He-Man and She-Ra have ended up, and would be a more likely scenario (and would be better than paying $$ for a download!)
Ok, voice is hoarse, stepping off my soapbox now!