1: Genesis Of The Daleks (4th Doctor)
It was hard to pick between this one and my second favourite but damn it, the origins of the Daleks and the debut of their psychotic creator really won out for me in the end. The Nazi allusions aside, this was an incredibly important story in the series history. Ethical debates on viruses aside, the Doctor had the chance to wipe out the Daleks and chose not to and Michael Wisher certainly brought a level of menace to Davros.
2: The End Of Time (10th Doctor)
The last story for David Tennant as the Doctor was always going to ignite strong debate but personally, I think it served as a good way of ending his tenure and briefly introducing Matt Smith at the end. The cameos from companions like Rose, Martha, Donna, Jack, Sarah Jane and Mickey were nice, Wilfred was a great support system for the Doctor and John Simm's return as the Master ticked all the right boxes. Even the disappointment of the Time Lords (Rassilon in particular) can't hinder this story that much.
3: The Five Doctors (5th Doctor)
Technically four because Tom Baker's contribution is lifted from a scene of uncompleted/unaired story, Shada but having the majority of the Doctor's incarnations, along with prominent companions and baddies like a Dalek, Cybermen, the Master, Raston Robot and even Borusa kept this special celebration of the series 20th year more than entertaining. Plus the line the Master says about a cosmos without the Doctor is unforgettable.
4: The Empty Child/The Doctor Dances (9th Doctor)
Easily the best story from Christopher Eccleston's short run on the series, this one is the perfect explanation as to why Steven Moffat is now running the series. Scares, chills, humour and a dollop of sexiness courtesy of Captain Jack Harkness and with his addition, we have the best TARDIS trio in quite a while.
5: The Caves Of Androzani (5th Doctor)
There was no way that this story was not going to make this list. As a regeneration story goes, it's got the right length of time, it's pretty dark in places and like certain future regenerations, you have the Doctor giving his life to save his companion. Plus you have a few interesting cameos appearances as Five begins his change into Six. Now that's done, let's all go and enjoy Eleven's first proper story tonight, shall we?