In general, so long as you keep them in character, there's no problems using villains from the show in your threads. This is assuming, of course, that no one plays them. It's a site about Time Travel: Villains can be encountered multiple times even after they died in show. Heck, even in canon, the Celestial Toymaker's timeline bounces like mad around the Doctor's. Just try to keep their motives and their general characters in tact, and they can be usable.