This list will be sticking to the new era of Doctor Who starting from 2005 with Christopher Eccelston as the 9th Doctor to 2013 with Matt Smith as the 11th because we have yet to see Capaldi in action and I haven't seen enough classic episodes to have a fair opinion of them.
10. The Army of Ghosts/Doomsday
Daleks are in almost every series of Doctor Who now and have slowly become less of a threat because of it. The show seems to enjoy pointing out as many flaws as possible about the supposed "supreme beings". However, Dalek was the first time we saw a Dalek in the new era and it is still the best Dalek related episode so far. At this point in the show, the game is simple. One Time Lord vs one Dalek. No complications, no deus ex machina, just pure fear. The first moments when The Doctor realises what's going on and is as scared as he's ever been should set the bar of what a Dalek's presence should mean. They should be feared and yet, this episode also highlights the fact that they aren't just mindless machines. In fact, they are living organisms for feel and have needs....yet still need orders and a Dalek without orders leads to a one Dalek army. Don't lie, you freaked out when you first saw it levitate up the stairs. While they have been overused now, I can still look back on their first appearance with fondest...even though this episode is now set in the past (this one is set in 2012...ouch).
Doctor Who is a show that, in it's heyday, was infamous for scaring the living daylights out of audiences and leaving them hiding behind their sofas. Excluding the next entry since I didn't even know what Doctor Who was, I have screamed twice watching it. The Forest of the Dead with all that Vashta Narada and deformed gltich people business and Blink for the God damn Weeping Angels. Sure, they have lost their appeal because Moffat won't stop milking them but when they first appeared, you can bet they left an impression. Acting as a 'Doctor-lite' episode as he barley makes an appearance, we see clever mind games involved in guiding Sally Sparrow (believe it or not, played by Carey Mulligan) to the TARDIS as The Doctor and Martha have been ambushed by Weeping Angels and send back in time. Nightmare fuel ensues as Doctor Who adds statues to the list of things we are now afraid of. Don't think that ending didn't make us paranoid.
7. The Empty Child/The Doctor Dances
5. The Girl in the Fireplace
Who ordered their episode that delivers a massive gut punch and leaves you in a pool of your own tears? The Girl in the Fireplace is the episode for you. Something that Doctor Who hasn't really done (as far as I know) is having characters get emotionally invested in a historical figure. Fires of Pompeii did well with Donna feeling sorrow for the doomed citizens of Pompeii (including Peter Capaldi and Karen Gillan...seriously) however it was The Girl in the Fireplace that perfected it. The Doctor, Rose and Mickey travel to an abandoned spaceship to find a time portal that takes The Doctor through to France throughout the 18th century and grows a relationship with Madame De Pompadour. The catch is that what may seem like minutes on the spaceship is years in France. As you might guess, there is only one way it can end and leaves us on one of the saddest notes of the series.
3. The Sound of Drums/Last of the Time Lords
I suppose you may be wondering who or what my favourite Doctor Who baddie is. After all, they can make or break an episode. I can reveal that my favourite is The Master. It may seem quite cliche to simply pit a hero against an evil version of himself (okay, there's more to it...he's not the Valeyard) but this is the episode that completely turns that on it's head. The reason this episode works so well can be summed up in it's first scene. The Master has already won. Right as the episode starts, he is already in power and in control. The Doctor has no TARDIS, he, along with Jack and Martha, are on top of the public enemy list and The Master is almost ready to decimate the human population. The stakes are the highest they have ever been and we see The Doctor fall into the mercy of his maniac of a former friend. The Master's insanity is explored with great depth and almost becomes sympathetic if it weren't for the constant barrage of evil and shocking strokes of psychotic torture and desolation. A truly thrilling romp from start to finish that ends on a bittersweet ending thanks for beautiful music and some of David Tennant's finest acting.
2. Vincent and the Doctor
I may be making myself out to be a David Tennant fanboy with no broad scope on this list. That's only partially true. Yes, he's my favourite Doctor but I still have place in my heart of Matt Smith as the 11th Doctor. I am aware that the best episode that highlights his Doctor is The Beast Below...or The Rings of Akhaten but I will tell you why Vincent and the Doctor does so many things right. It nails what the show was supposed to do in the first place and that is explore time and highlight historical figures as well as explore their real life turmoil in a fresh way. Vincent Van Gogh is played wonderfully by Tony Curran and we see his real life suffering portrayed in a heart-breaking fashion (the ending still hurts) tied in wonderfully to the narrative by making great use of his talent and unique mind. However, there is one moment that lets this episode skyrocket up the list and that is when The Doctor takes Vincent to a museum showcasing his artwork. Whoever chose the music for this scene deserves a bloody raise because I can't hear that song without getting teary eyed. The music, the acting and even the cinematography is beautiful and is probably the most emotional I've ever been watching anything. Yes, I cried....every time.
1. Human Nature/The Family of Blood
For many years now, I've been parading about claiming that Vincent and the Doctor is my favourite episode...that is until I stumbled upon this masterpiece when re watching the show. This is the episode that cemented The 10th Doctor as my favourite fictional character. We are shown an impossible vision of The Doctor living a human existence with no memory of his life as a Time Lord and having to deal with real human issues having now been torn down to our level. Love, loss, regret, pride. It conveys that, while from another world, he is still human at heart. The parallel's between The Doctor and John Smith make for wonderful commentary and are introduced to an enemy clearly out to destroy The Doctor's livelihood and everything he cares about as well as being introduced to Joan Redfern who works alongside John through is identity crisis in an archaic but lovely setting. In a way, it proves that anyone can make a difference and there is true power stored in even the smallest man. This is a truly inspiring episode but it's the ending that solidifies this as number one for me. The Fury of the Time Lord. One thing is for certain: Don't. Mess. With. The Doctor. He is a force to be reckoned with. He's labelled as the Oncoming Storm for a reason. This is the episode that makes me realise that he isn't really a hero...but in a good way. Hero is a label, it's just a title. The Doctor can antagonise, he can save galaxies and entire civilizations, he can destroy people's livelihoods through one sentence or action. A major case of "Be careful what you wish for" tied up with a perfect ending that pulls together aspects from earlier points in an effort to say "this was going somewhere". A well thought out, beautifully written episode that captures the true essence of The Doctor and the show as a whole. And two Game of Thrones actors helps.
Also the Scarecrows were cool.
Love and Monsters
The Doctor's Daughter
Silence in the Library/Forest of the Dead
The Rings of Akhaten
The Sontaran Stratagem/The Poison Sky
It would appear that from all these episodes that Series 3 is evidently my favourite. I can't quite make that claim but it certainly delivered some tremendous episodes, didn't it.