Steven Moffat boldly takes Doctor Who into the modern age with a tale of evil lurking in the WiFi. It turns out though that the enemy is really The Great Intelligence, who seems to be playing a big role in Series 7. This story also introduces the 21st century Clara Oswald, the great new companion to the Doctor.49. Attack of the Cybermen
The first story of Colin Baker's first full season as the Doctor had a lot to live up to after his disappointing introduction story. Fortunately, his aggressive nature is toned down and we're treated to an intriguing tale bringing the Cybermen back down to the suers and back to Telos, their two most familiar homes. This story is also infamous for the Doctor shooting a Cyberman, but if you watch the story, who can blame him?
48. The Chase
I'm not a huge fan of the William Hartnell era, so The Chase is his only entry in my Top 50. This is however a rather funny and odd Doctor Who story, having the Daleks chase the Doctor and his friends throughout the galaxy in a overtly comedic way. It sees the saddening departure of Ian and Barbara.47. The War Games
Patrick Troughton got an epic send-off as the Doctor, in this huge 10 part story featuring different wars from throughout history all clumped together under the rule of the War Chief and the War Lords. Turns out he is one of the Doctor's race, the Time Lords, who are the only ones who can put an end to the evil at hand.
46. The Stones of Blood
Part of 1978's year long Key to Time arc, The Stones of Blood is my favorite entry from that season. It features some wonderful modern day bits, along with some good atmospheric sections. The leads are great on all accounts, with great stuff for Tom Baker, the beautiful Romana I, and K-9 being his doggy self. And what better than having the baddie be a beautiful silver lady?