45) London finally gets nuked, in "Turn Left."
We finally get to see what things would be like without the Doctor and... not that great, actually. London gets completely pulverized, and you get an awful glimpse of the evil the Doctor is always standing in the way of.
44) The Doctor saves his ambiguous wife, in "Forest Of The Dead."
I had some issues with the way women were treated in this episode, including the "happy ending" River Song gets treated to. But you can't really beat the Doctor jumping down through the entire library, with one bar left on the buffer thingie, to restore his "wife" from a saved backup before she's gone forever. Can you?
43) Bannakaffalatta stops the angels, in "Voyage Of The Damned."
Cyborg pride represent! Don't let anybody tell you you're inferior just because you're part machine. You can bring down angels!
42) The Master's musical number, in "Last Of The Time Lords."
This is possibly the greatest moment in Doctor Who history, and the episode where I finally decided to stop worrying and love the Russell T. Davies era. The Master seranades a hyper-aged Doctor after he's conquered the planet Earth.
41) The DVD extra conversation, in "Blink."
Sally Sparrow actually manages to have a two-way conversation with the DVD easter egg that the Doctor recorded in 1969, thanks to his handy transcript.
40) The TARDIS car chase, in "The Runaway Bride."
Catherine Tate is being kidnapped by an evil Santa taxi-driving robot, so the Doctor manages to steer the TARDIS along the highway. Just totally insane.
39) Dalek-Cyberman smackdown, in "Doomsday."
Haven't you always wanted to see the Cybermen fight the Daleks? If the Daleks could fly?
38) The weird ELO cover band, in "Love And Monsters."
Sometimes the Doctor changes people's lives without even knowing it — like this group of loners who come together to play ELO in his honor. Too bad that mean alien guy ruins it.
37) The mirror stunt, in "The Girl In The Fireplace."
The cavalry arrives — literally, on a horse. Through a mirror from an alien spaceship.
36) K-9 finally shows his bite, in "School Reunion."
As an old-school fan of K-9 the tin dog, it's great to see him finally going ballistic and shooting down tons of killer bat creatures instead of creaking along. And then Giles from Buffy says "Bad dog," and K-9 says "Affirmative," and blows him up. Classic.
35) "It. Is. Defended!" in "The Christmas Invasion."
Another lovely defiant Doctor moment. He defeats the Syccorax in single combat, despite losing a hand along the way, and then gives a great speech telling them to tell everybody about the Earth's riches and wonders, and then tell all the nasty alien conquerors, "It. Is. Protected!"
34) The Doctor's defiant speech, in "Bad Wolf."
A lovely bit of defiance and brio, as the Doctor tells the Daleks he's going to rescue their hostage — and they're so shocked, they don't even think to execute her.
33) Captain Jack's naked showdown, in "Bad Wolf."
Where do you think he kept that gun?
32) "Everybody lives," in "The Doctor Dances."
The Doctor not only figures out why people are turning into gasmask-clad child-brained zombies, he manages to reverse it and save everybody. He's just so bright and in this episode.
31) Captain Jack rescues Rose, in "The Empty Child."
She's only in 1942 for a few minutes before she gets lifted up by a barrage balloon and winds up falling out of the sky... but Captain Jack, in his most swashbuckling moment ever, catches her with his spaceship. Awesome.
30) The Doctor regrows the TARDIS, in "Father's Day."
Rose has wrecked the space/time continuum, thanks to her daddy issues, but the Doctor is able to use the TARDIS key to regrow the TARDIS inside the church where everyone is sheltering. Too bad Rose messes things up again.
And the countdown continues at io9