Shirou Kamui and Monou Fuuma, the two teenaged "kamuis" who are ultimately responsible for humanity's fate.
The Chi No Ryuu or Dragons of Earth. The apparent "bad guys" of X, whose role is to wipe out humanity so the earth can have a fresh start. In my opinion, a hell of a lot more entertaining than their counterparts.
The Ten No Ryuu or Dragons of Heaven. The ones fighting to save humanity. The cause they defend, although very understandable, is actually not very cosmologically correct.
Everyone else that plays a part in the story, from the Clamp Campus Detectives trio, to the irrepressible Segawa Keiichi, and even a certain little girl and her stuffed frog...