Following up on The Orr Group's Roll20 recent usage statistics, I've just gotten some figures in from Smiteworks, who make Fantasy Grounds. Fantasy Grounds is, of course, the officially licensed Dungeons & Dragon virtual tabletop, and so its usage figures reflect that, with a very dramatic lead for D&D - the most popular systems, in order, are D&D 5E, Pathfinder, D&D 3.5, D&D 4E, and Savage Worlds.
Taking 5E out of the equation, the other games make for an interesting list.
Taking 5E out of the equation, the other games make for an interesting list.