The closest thing to a Dragon in Xenogears, and even then, I would argue he's more of a deconstruction of the trope is Ramsus. Margulis from Saga is pretty much a Dragon as well.

Saren from Mass Effect was a great one, as was Queen Zeal. Golbez is pretty awesome as well even if you think he's only revealed to be the Dragon after Zemus pops up in the story.

Course my all time favorite, even though most of the time he turns out to be the Man Behind the Man trope, is Revolver Ocelot.