And here's Part 2 of the list
41: The Fires Of Pompeii (10th Doctor)
Moral dilemmas on Who are a big deal and putting the Doctor and Donna in the situation where they couldn't prevent something like Pompeii certainly raised some interesting moments between the pair. Oh and see if you can spot Amy Pond in this one.
42: Pyramid Of Mars (4th Doctor)
Regarded as one of Tom Baker's best stories, this one certainly hits the right spots. How come we've never gotten a televised follow up to Sutekh, given how he promised to kill the Doctor but not yet? Maybe it's something for Steven Moffat to consider writing.
43: Smith And Jones (10th Doctor)
Arguably the best opening episode of the new series and all because the focus is brilliant. Martha endears herself as a resourceful and wonderful companion, the Doctor's on fine form, tricking Florence the way he does and like the Ood, the Judoon make a brilliant first impression. And there are those hints about a certain Mr Saxon as well.
44: The Unquiet Dead (9th Doctor)
Ghost stories are always a nice to do, even on a show that technically doesn't indulge in ghosts and ones that feature Simon Callow as Charles Dickens is another reason why this story is made of win. Plus, I was beginning to feel the Doctor/Rose connection here.
45: The Mark Of The Rani (6th Doctor)
Another underrated story IMO. The Rani made a good impression in this one, Six and Peri's bickering wasn't as bad and the Master's actually fun, even if he is undoubtedly shoehorned into proceedings. Plus, the Rani knees him in the nadgers at one point.