I mean the Doctor is a tough cookie to crack, but anybody who has similar abilities such as genius and time travel and/or time abilities and has taken on and beaten bigger threats than the Doctor should win. Again I'll say Doctor Doom, Dr. Strange (classic for sure, maybe not modern), Dark Schneider because of dispel bound, Giorno and maybe Enrico Pucci from Jojo, Thanos as the Avatar of Death, and probably Batman and Lex Luthor with immense prep. Now Giorno might be a chart character so scrap him if you want but most I the others I named are capable of taking down the Doctor. Oh, and from Doctor Who of course, the Master. He's won and lost before though so 50/50 for him.