1 - The Empty Child/The Doctor Dances
2 - Midnight
3 - The Impossible Planet/The Satan Pit
4 - The God Complex
5 - Heaven Sent
In spite of common opinion I don't actually think that Doctor Who does 'scary' very often - and not just because I don't find it scary (to be fair a family show shouldn't be aiming to traumatise) but because it so seldom decides to pile on the scares quite so mercilessly.
Heaven Sent isn't in and of itself a scary episode (in fact Series 9, despite being the 'darkest' series of the lot in many ways never strays too far into scares) but its idea is scary. Imagine being trapped and alone in a castle like that and
not being the Doctor. Constantly outrunning the Veil is your only purpose in life, staying one step ahead of the game is your primary goal, and if you're very lucky you get to chip away at a near-impenetrable wall. Quite the metaphor for life really, and with the added skulls and buzzing flies and the sense of isolation and loss from Clara's recent demise it hit the right creepy notes when it had to.
The God Complex is a rather underrated story I feel - but then I rank it as one of the best of the past decade. It's depends far more on how you perceive it rather than actual scares more so than any other episode on this list. It has its odd jumpy moments, but the scares lie in its conceit.
The Impossible Planet/The Satan Pit delivers a mix of physical and psychological scares. The whole thing is seriously dark in places, and at its best when it challenges the faith of the crew - getting into their minds with some questionably vague therapy tricks. The Beast is a scary villain in the flesh and in the mind, the Ood make the whole sanctuary base feel very claustrophobic and the very idea of actually finding 'the truth behind the myth' of any God or Satanic being is quite a daunting, scary idea.
Midnight's scariest aspect is that we never get to find out quite what it was out there - a fear of the unknown. I was rather fond of the idea that the unseen entity in Series 8's
Listen (another episode with creepy moments) could very well have been one of the same species - a creature with perfect camouflage. I don't want a definitive answer, which would spoil the unique spot that Midnight earned. It had its fair share of jump scares, but ultimately it was watching a bunch of ordinary and mostly friendly people turn on each other through the mere power of words and suggestion.
The Empty Child and
The Doctor Dances were the original 'play on something ordinary' from Moffat, and considerably his finest effort in that regard. The wartime backdrop added a real atmosphere to it, the transformation process as seen on Doctor Constantine was horrific and the right side of painful looking without being overly traumatic, and above all it balanced the sense of fear through jumps and careful consideration of the scary idea it explored. (This was the only Doctor Who story to ever creep me out as I watched it - in my defence I was at my youngest obviously when I watched it too

).
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Honourable Mentions...
Blink deserves a mention even if it's not as creepy as it's often billed as being. It depends a bit too much on jump scares - which once you've seen it more than once you know where they're going to be. Nonetheless the concept is still rather creepy too, albeit in a more psychological way than most of the scares on the list.
The Waters of Mars is up there for its creepy concept. A villain you can't argue with or reason with, it's an uncompromisable force and indiscriminate in who it kills. The episode proves to be quite a bloodbath, and it was where the episode was at its strongest. If it hadn't had some awkwardly wonky and cheap shots of the zombies running through corridors like they were going for an evening stroll it would have been far more effective and would have earned a spot on the list.
The Beast Below had all the markings of a dark and scary story. It never quite chooses one idea to fixate on and explore in more depth, but the creepy English society of the future mixed in with the Smilers, and scary elevators as well made for a bit of a scarier episode.
The Doctor's Wife is the perfect example of an episode which has scary moments but that isn't quite what defines it. Amy and Rory go through a fair bit of psychological torture in the Tardis, whilst the Doctor encounters some rather grim stuff whilst on House. Idris is the focus of this piece though, and she's about as scary as Matt Smith in a ball pit.
Asylum of the Daleks gave a hint of just how well Moffat is capable of writing the Daleks, but it's again all quite psychological. Oswin was a real highlight of Series 7, but a part of that comes from the tragic twist that befell her character. If you want the most terrifying creature in the universe to roll around with a plunger and a whisk to be taken seriously, this is how you do it.
The Witch's Familiar expanded upon the creepy concepts behind the Daleks much further, but again you have to read between the lines to realise just how horrifying it all is. That makes the episode indirectly quite scary, but all the same the idea of the Daleks being brutally self-conditioned into hatred makes the whole concept of removed emotions much more terrifying an idea than it ever was before - the kind of scary ideas that go over the heads of younger viewers but actually make for intriguing watching for older ones.
Under the Lake and
Before the Flood both played on rather traditional ideas of fear but they worked pretty well. The base itself was claustrophobic, whilst the ghosts were an unpredictable and hard to pin down threat. The Fisher King lurked in the shadows for a long time before he revealed his gruesome self, and even then had some horrifying ideas about humanity being in chains that he was happy to share. The highlight though being the dragging-along-the-floor axe moment... the tense scene played out perfectly in terms of scares, timing and atmosphere.