42. Silence Of The Library/Forest Of The Dead 4.8-4.9
To talk about Rose as being very much a product of its own brand of Doctor Who, I felt it was equally appropriate to find a story that did the same for the current era. This story is very much that adventure. The events of the Library are the epitome of creepy and dark Doctor Who, preying on some of the most intrinsic human fears with this flesh-eating insect swarm, the Vashta Nerada, who group in shadows. It also features a manipulative interior world, and a truly terrifying combination of visceral and psychological horror. It also serves as the start of many features of the current era of Doctor Who including a penchant for complicated mystery and intrigue mainly by being the first appearance of the enigmatic River Song. It also cements a trend where death is an impermanent state, many stories in the Eleventh Doctor's era have characters who share this surviving beyond death quality.
41. Feast Of Steven (Part Of The Daleks' Master Plan) 3.16
The one exception on this list where I recommend a single episode rather than a complete story arc. This story within a story features companions Sara Kingdom and Steven Tyler, and the Doctor getting rounded up by police and then stumbling in on an early movie set. There are multiple cases of mistaken identity, and all sorts of related chuckles. It is a highly predictable spoof of some Hollywood clichés and the amount of everyone speaking at once would be headache inducing if it went any longer, but it is delightful nonetheless. Best of all it features the Doctor wishing us all in the audience a Merry Christmas, a sweet precursor to the intense way Doctor Who celebrates Christmas today. The surrounding serial in which Feast of Steven is contained, if you like reconstructs, is incredible. It is more of the old school Daleks, and in addition to Steven and Sara also contains the literally short-lived Katarina. This serial proved companion death was possible. It also features the Meddling Monk marking the first villain return, and was the first appearance of incredibly long-time companion the Brigadier.