From what i've heard, capturing five (5) of each monster in the game and the Monster Anrena guy will give you 99 dark matters.

Fighting the Dark Aeons also nets you 1 (or 2 for an overkill) Dark Matter(s). But if you have the American version of the game, this is out of the question.

Can't really say if there's any other way to get them. There are prolly lots of way, but none that i can think of at this time.