Because it's a hard task anyway, I'll ease my burden by carving it up into categories:
1. "The Invasion."
I can never say enough good things about this serial. I love the 2nd Doctor, Jamie, & Zoe. I love Tobias Vaughn. I love Isobel Watkins. I love the Brigadier & UNIT. I love the animated replacement episodes for parts 1 & 4. I simply love it!
2. "The Romans."
One of the few out-and-out comedies the show ever did.
3. "City of Death."
Douglas Adams at his best. Tom Baker keeping things light but never getting too silly. It's a shame this is really the only decent story in all of Season 17. "I say, what a wonderful butler. He's so violent."
New Series, Russell T. Davies Era
Such a brilliant, creepy bottle episode. I wish they would do more episodes like this where the Doctor feels truly threatened and outside of his comfort zone.
Just a great piece of timey-wimey science fiction.
3. "Human Nature"/"The Family of Blood."
While the Davies era seemed to run out of ideas pretty quickly, I think this episode was a great exploration of a new side of the Doctor's personality. And I love the way the nurse totally calls out the Doctor at the end, "If the Doctor had never visited us, never chosen this place on a whim, would anybody here have died?"
New Series, Steven Moffat Era
1. "Amy's Choice."
I love it when the show does something different and plays around with its own format. In this case, I love the fact that they have to choose between the 2 separate realities. The Dream Lord is a great villain. Plus:
2. "The Lodger."
More variety with the format. In this case, Doctor Who
as a domestic sitcom. One of the reasons why Matt Smith is among my favorite Doctors is because neither Eccleston nor Tennant could have pulled off this episode.
3. "Vincent & the Doctor."
It nearly makes me cry at the end when Vincent finds out how famous he is in the future. (And, as a fan of the Underworld
movies, it's nice to see Viktor & Markus getting along for once.
Big Finish Audio Adventures
It perfectly exploits the audio format because the Doctor & Charley are blinded for most of the story. Plus, I love how well McGann conveys the frustration of loving someone at an inconvenient time.
2. "The Natural History of Fear."
The twist at the end of the story is another great example of exploiting the audio format. It's a very trippy journey into a dystopian dictatorship where the Doctor is either a brutal government functionary or the secret leader of the resistance. No Doctor can go dark-side quite like McGann.
It's one of the trickiest time travel stories that the franchise has ever done, with the Doctor & Ace accidentally changing the outcome of WWII. (Listen for a pre-Doctor David Tennant as a nasty SS officer that keeps threatening to rape Ace.)