Obviously Montalban. Hugely captivating and memorable.
Cumberbatch's John Harrison had the potential to be a great villain in his own right but the Khan revelation completely neutered him. The actor gave a great performance though, and with a better script he'd have given good competition. As it stands, he's kinda a generic modern blockbuster villain in the mould of Ledger's Joker, Loki from The Avengers, and Silva from Skyfall. Though they were much better.
Khan. The fact originally conceived villain John Harrison turned out to be Khan in a contrived twist, was incidental to the storyline and amounted to a gimmick. Quality will always beat gimmick.