Holy crap, that's hard.
I would say its definitely between Name of the Doctor, Blink, Empty child, Eleventh Hour, Time of Angels, Silence in the Library, Let's Kill Hitler, Time of the Doctor, Asylum of the Daleks, A Christmas Carol, The Girl in the fireplace and Deep Breath! :P
Damn, I cna't choose, and since the title doesn't specify his best episode of which show let's jsut cheat and say it's A Scandal in Belgravia

Or His Last Vow... or possibly A Study in Pink...
Re: Girl in the Fireplace being mawkish: irrelevant. We're talking about 'best', not 'favourite'. Your taste is irrelevant. That script is masterful. It's a fantastic concept (sure, swiped from 'The Time Traveller's Wife' ) and it's fully realized and followed through. There's no cop-out, or magic fix, unlike msot episodes of Doctor Who. And damn it, it's like clockwork: every line resonates and every plot detail makes sense. I rewatched it last week, and it's an episode I appreciate more every time I see it. The final shot with the reveal of the name of the spaceship never fails to excite me. There are no flaws in that script. Not a single one. I say this as someone who doesn't even consider it one of his favourite Moffat episodes.
Saladfingers: I also rewatched Silence in the Library and you're totally right: for being the less talked about of Moffat's pre-showrunner episodes it's staggeringly right in nearly every department. It gets the Doctor Who formula absolutely right and balances all those different attributes into one proper piece of actual science-fiction that also has all of the character drama and romance anyone could want. Holy shit.