1. Face the Raven/Heaven Sent/Hell Bent
Heaven Sent alone is enough to put this at the top for me, but that's not to dismiss the other two. I thought these three episodes did a fantastic job of putting the Doctor and Clara's relationship to a close. I loved the angle that their friendship was actually something quite destructive, but still sweet. Hell Bent was flawed but not bad: it really ought to have been two episodes, and Gallifrey needed more time, but it did a great job of finishing Clara's story and showing a Doctor who'd gone of the rails in a sympathetic light. Heaven Sent, though, is single-handedly the best episode of New Who and I'd be very surprised if anyone could top it. Capaldi was absolutely astounding and gives his most defining portrayal of the Doctor yet, one which I find to be the truest to the character in the modern era.
2. The Pandorica Opens/The Big Bang
Never liked the whole "Let's have a cameo of loads of enemies thing" but this was a firm reminder for me that Moffat's era was going to be special. For once, we didn't get an over-the-top, excessively loud finale that was yet another Dalek/Master invasion of Earth. It was ridiculous, frantic, needlessly complicated, but it was great. The absurdity of seeing Amy's death ruined by the Doctor appearing with a mop and fez, and then the satisfaction of seeing him fulfil that scene later on, is just great. Moffat also decided that nearly destroying the universe wasn't enough, and actually went ahead and destroyed... but the explanation for recreating it, though ludicrous, is still brilliant.
3. Dark Water/Death in Heaven
Capaldi's series seem to have a pattern of the penultimate episode being better than the final one. Not that Death in Heaven was bad, but Dark Water was a lot better. Unlike some I loved the scene where Clara tries to destroy the TARDIS keys, and this Doctor who we've seen to be grumpy and antisocial since his regeneration forgives her and tries to help her, to help the person who had been the only one he could open to and show emotion through at times. I didn't like the Missy revelation at first, but she changed my mind immediately with the next episode... like a mix between Simm and Ainley, eccentric but sinister, and there's a very twisted bond between her and the Doctor. Worth mentioning is the "Don't burn me" scene: spine-tringling and horrifying, but that's what was great about it.
4. The Name of the Doctor
A quite good finish to a series that was a little disjointed. This episode took more of an epilogue angle, I think, which didn't work too bad. Richard E. Grant was great as the GI, but the Whisper Men were an occasional Moffat problem where he gives us a great concept but doesn't explore it too well. The Clara resolution was unpredictable but made a lot of sense, so I think that worked out well.
5. The Wedding of River Song
As much as I loved Series 6, my favourite of Matt Smith's, this is easily the lowest of Moffat's finales. One episode isn't enough to solve the hefty amount of puzzles throughout the series and still tell a solid story. As fun as the whole history mix-up was, it was all too rushed that it felt difficult to catch a breath. I think this just comes up over the S1 finale for me because I care more about the characters in this one and enjoy the style a lot more.
6. Bad Wolf/The Parting of the Ways
Easily the better of RTD's finales, as it did a good job of bringing things to a climax and finishing the Bad Wolf theme. The part where the Doctor tries to blow up the Dalek ship was, I admit, excellently done and Eccleston sure knew how to do a regeneration scene. Rose becoming Bad Wolf and disintegrating the Daleks felt a little too convenient for me, and the line "I think you need a Doctor" was enough to give me violent convulsions. I really don't think it needed to go down the cliché route with the Doctor kissing Rose, after the series did a good job of establishing them as close friends.
7. The Stolen Earth/Journey's End
An improvement over the last few finales, yet still overstuffed and overblown. I think it helps to have an appreciation of RTD's characters to enjoy this, but for me it was a bunch of characters I didn't care for struggling to make room on set. Davros' return only proved he still suffered from post-Genesis blues of being written as a not-so-complex caricature of a mad scientist, and negative points for bringing Rose back after no time at all and acting like it was the best thing that ever happened to the show. The Bad Wolf Bay II scene was awful, but admittedly the regeneration cliffhanger and Donna's exit were handled quite well.
8. Utopia/The Sound of Drums/The Last of the Time Lords
Utopia was a much better start than what the two finishing episodes continued. I didn't enjoy Simm's Joker-like portrayal of the Master, that felt kind of like what Ramsey now is to Game of Thrones, where every scene takes the opportunity to say "Look how crazy this guy is" The last episode had potential because of a great premise, that gave the criminally misused Martha a chance to actually shine, and it didn't start too bad, but it all fell apart with one of the most ridiculous and cringey resolutions I've ever seen from Who. Everyone in the whole world happens to pray to the Doctor (because this era seemed to enjoy making Jesus metaphors from him) and this magically de-ages him. Then he hugs a sulking Master, which looked quite funny. Finish it all with everything that happened in the last two episodes being undone anyway, thus there was no real consequence except the Doctor could talk about how lonely he was even more. How this episode came about, I would not like to know.
9. Army of Ghosts/Doomsday
Nail in the coffin for what is one of the worst series in Doctor Who in my opinion. It was the start of RTD trying to outdo his preceding finale in epicness each year, only to have an awkward mesh with his odd sense of humour and a LotR-like soundtrack. The Dalek and Cybermen war didn't deliver at all, and Rose and the Tenth Doctor, one of the most unlikable duos in the show's history for me, are cut off by a literal wall, which I assume is supposed to be symbolic. Then we have the Bad Wolf Bay scene, a scene which tries so hard to tell you what to feel that between that and the loud, sad music, and the sight of the Doctor being in love with a companion in one of the most clichéd ways possible, I felt ill.