I would have to say that my top three favourite episodes/stories from the Eccleston era would be Dalek, The Empty Child/The Doctor Dances and Fathers Day.
For the Tennant era they would be Human Nature/The Family of Blood, Silence in the Library/Forest of the Dead and The Waters of Mars.
Matt Smith's best three (for me) would be The Eleventh Hour, The Doctor's Wife and Amy's Choice.
Best Multi-Doctor Story?
The Day of the Doctor. Clever, epic, humorous, satisfying and filled with brilliant and subtle references, it just blows away the competition.