1 -
Bad Wolf/The Parting of the Ways
A solid opening episode, followed by a spectacular series finale that has not been bested in a decade. The Daleks had real menace and character, the Emperor an intriguing and fascinating religious nutjob, and the Doctor and companion pairing was strong with this one. Chuck in Jack Harkness, an epic-scale story that wasn't on contemporary Earth and the resolution to a successful, iconic story arc and this easily sits atop.
2 -
The Stolen Earth/Journey's End
Crammed so heavily with characters that it collapses under its own weight in its second half, this packed a hell of a punch as stories go. The most rewarding aspect was the convergence of so many likeable characters...if this finale were a Marvel film, it's The Avengers... but better

A shame the second part didn't live up to the first, but Davros was still a fantastic villain, Donna got a tragic but superbly acted send-off and it was just an absolute blast.
3 -
The Pandorica Opens/The Big Bang
Two very distinct episodes, and very different from each other. But both were extremely strong, if neither actually perfect. The scale of the first episode was superb, and it was a nice touch to see things scaled back in the second half - which more or less carries itself on the four main characters. It was bold, and grand and perhaps a little let down by two companions who hadn't been anywhere near as likeable as Donna, Martha or Rose before them. It also lacked a clear, identifiable villain which at the time worked, but knowing where it all eventually heads is a bit of a dampener.
4 -
Dark Water/Death in Heaven
A decent premise, and a welcome return to the two-parter above anything else. Another finale where the latter half brings the first half down, the plot ultimately seemed to go nowhere and the whole thing was rendered redundant - also chucking in a few moments better off forgotten (CyberBrig? Really?!). The cinematography was consistently good as least, as was the direction. It was just story that dragged this down, which is a shame as the first half was absolutely superb and delivered some of the best ideas and developments across the Moffat era.
5 -
Army of Ghosts/Doomsday
A respectable and decent story, in fact there's very little wrong with this one at all. It's only real issue is that it felt like a poorer replication of the Series 1 finale. We'd already seen a Cyberman story earlier in the series and this one didn't do very much to differentiate itself. Chucking in Daleks was a good idea, but the confrontation was a largely wasted opportunity and their invasion less impressive in terms of spectacle and dramatic impact than it had been a series earlier. There were some superb character moments though that still make it worth rewatching.
6 -
The Sound of Drums/Last of the Time Lords
It's hard to pinpoint what didn't work about this finale, and opinions often vary about it. For me I had no problem with the whole 'God-like' ending in the second half, my personal issue is more with the potrayal of The Master. I felt that whilst John Simm did a great job, they took the comedy aspects a little too far with his character - which would have been fine if it didn't jar with the serious tone of the rest of the story. It also felt odd to cast a young Master who was meant to be a dark mirror image of The Doctor, only to keep the Doctor aged and elderly for the duration. Add into that a dissatisfying conclusion for Martha (I'd rather have had The Doctor stranded on that cliffside off of the Valiant when time reset, as it would have given her more reason to leave when he couldn't appreciate the value of what she had just done for him) and despite a decent, and above all different premise, too much wasn't quite right with this one.
7 -
The Name of the Doctor
Somewhat let off of the one-part finale doesn't work argument because it leads into the anniversary special, this story was decent and it was great to return to the formula that afforded us a clear and present villain, and a series-spanning story arc. Unfortunately at just one part, the Great Intelligence as a villain felt tacked on and a bit of an after-thought - lacking any real depth. Clara at this point had not been sufficiently fleshed out because of her story arc, which had disappointed - I always thought it would have made more sense for River to be the one to enter his time stream (if written a bit differently so she were alive - it'd be a great way to explain their close connection). This was a finale that didn't really pay off as a finale should, but it did okay as a typical episode.
8 -
The Wedding of River Song
One-part finales don't work. In a show that can go anywhere and anywhen, you need to afford the concluding story extra time to explore its premise in greater depth...it needs to be richer, and more rewarding. This was not. In fact it was the poor footnote to a poor story arc that consumed the sixth series - which was salvaged merely by the amazing strength of its standalone stories. It was full of problems, was unfulfilling and the most unsatisfying conclusion that Doctor Who has ever had. It all seemed done for spectacle - Moffat gets certain images in his head, like balloon-hoisted cars across London (and what?!) and writes a story to accommodate it. We've thankfully come a long way.
And for reference if I was to slot in the two 'Specials' finales, then
The End of Time would slot in 9th place, behind every other story here.
The Time of the Doctor would probably slot in 6th place.