6: The War Games (2nd Doctor)
For a regeneration story, this was certainly longer than expected. 10 whole episodes with different wars being played out for perverse pleasure, a charismatic Time Lord foe in the War Chief and then the rest of the Time Lords being total bastards by forcing Two to change and wiping Zoe and Jamie's memories before sending them back to their own times. Plus the ending is rather haunting.
7: Human Nature/The Family Of Blood (10th Doctor)A thing that has occurred in the new series quite a bit is that some of the stories have been based on or have used bits from past books, audios and comic strips. Paul Cornell wrote this story for the Seventh Doctor and Benny and it worked second time around for Ten and Martha. A human Doctor who falls in love and has to give it all up to save the world, this is certainly one of the most sophisticated stories from the series as a whole.
8: The Stolen Earth/Journey's End (10th Doctor)
RTD sure did love his larger than life finales, didn't he? With this one, you have two Doctors, Rose, Martha, Donna, Jack, Mickey, Sarah Jane, Torchwood, K9 and Luke against the Daleks and Davros but none of that mattered. It was the heartbreaking way that Donna's memories had to be wiped away that got to me the most. Here's hoping that Amy isn't for a similar fate.
9: The Three Doctors (3rd Doctor)
Multi-Doctors are a big thing and the first one to gather Doctors One, Two and Three might be the most cohesive of the bunch. It was certainly a good way of debuting the series tenth year and Omega is one of the best Time Lord figures used in the series. Maybe not Master brilliant but he certainly had a presence in this story.
10: The Deadly Assassin (4th Doctor)
Probably the only genunely companionless story of the entire series for the Doctor, this is also one of the most violent stories too. The Master goes to virtually any length to prolong his existence and in dreams we see the Doctor nearly drowned at one point. Plus the ending is utterly brilliant when a certain someone lets his escape known.