I'll concur with "Everybody lives!" That is, indeed, a wonderful moment. I'll add a couple from "School Reunion": when the Doctor first sees SJS, and when he later tells her "Goodbye" (for the moment). Very heartwarming.
I'll also add:
-The Doctor and Grace say goodbye (the McGann Movie): the way the Doctor & Rose departure should've been handled, rather than beating the dead horse, resurrecting it, killing it again and beating it again.
-The Brig takes a stand against the Destroyer ("Battlefield"): perhaps his finest moment.
-The Dalek levitates for the first time ("Remembrance of the Daleks"): the Dalek moment we've all been waiting for, till RTD made them fly and it looked ridiculous.
-The Doctor nearly doesn't regenerate ("Caves of Androzani"): very dramatic, with the companions urging him on and the Master urging him to die.
-The Doctor leaves the party ("The Green Death"): a very bittersweet ending.
-The Doctor confront mad Xoanon ("The Face of Evil"): a very tense scene with one of the better cliffhangers.
-The Doctor mentions his family to Victoria ("Tomb of the Cybermen"): one of the earliest mentions of his family post-Susan, and a nice and angst-free character moment.
There are more, but I've got to get back to work.