Of the options given, the Master. I loved both the diabolical, nefarious classic versions and the complete nutcase of the new series.
I'd also nominate Davros, the Valeyard, Omega and the Black Guardian. Morbius and the other renegade Time Lords would have definitely benefited from more screen time as well.
EDIT: Special mention goes to the Wirrn (of The Ark in Space) for being the only Doctor Who monsters to give me nightmares.