To speak specifically as to soundtrack availability on iTunes, it's somewhat random. The best supported composers and series are almost fully available. Nobuo Uematsu and Akira Yamaoka have very robust selections available, and companies such as Square Enix and Konami seem to be making efforts to keep their selections vast and varied. Most Final Fantasy soundtracks and a number of arranged albums are available, but there seem to be various licensing snags that can affect their availability, as they come and go from the store. One of the most frustrating examples is the Final Fantasy XIII soundtrack. Most of the soundtracks can be purchased for between eight and twenty-five dollars, but FFXIII can only be purchased by individual track, because the vocal theme at the end (presumably) couldn't be licensed for release in America. (Interesting note: the Lightning Returns soundtrack is available already.)
As far as Nintendo soundtracks go, I can't think of any first-party titles that have any official soundtracks available, and I tend to check every couple of weeks. Otherwise, it's all third-party material. Amusingly, Opoona's soundtrack is available. (A game that all too few people know about). I really have no idea how well these sell, but they all seem to have a healthy number of reviews, and they all have high ratings.
Finally, sorry, Jonny, but the Brink of Time arranged album (which is incredible) isn't available. Only the Chrono Trigger original soundtrack.