12. Army Of Ghosts/Doomsday 2.12-2.13
Responsible for starting a tradition of truly epic companion departures, this two-parter is the story of how the Doctor comes to be separated from declared-forever companion Rose. Leading up to this novel and incredibly emotional separation, is a truly different battle for the Doctor where he faces not one, but both of his greatest enemies, the Daleks and the Cybermen simultaneously. So alongside establishing a need for pomp, circumstance and grand tragedy whenever a future companion leaves the TARDIS (ok, Martha's debatable), it's is the first time we see two major Doctor Who monsters coming together and it leads to a stand-off not only with the Doctor but among themselves. If nothing else, the combination was worth the Dalek-Cyberman slanging match alone.
11. Terror Of The Autons 8.1-8.4
Terror of the Autons was an easy choice for a couple of reasons, it is the first story to feature Jo Grant, who is best summed up at least initially by this line from the Brigadier: "Nonsense. What you need, Doctor, as Miss Shaw herself so often remarked, is someone to pass you your test tubes and to tell you how brilliant you are." Thankfully this era of attitude toward companions or assistants did not last long. It is also the start of the Master as the Master, who establishes himself from scene one as the puppet-using, life-as-tools-to-his-ends character he normally is. The Doctor's disdain for him is well established here, even before he and the Master meet again for us to see. It also introduces the feature of Time Lords to hypnotise, something that reaches a peak in the next Doctor's era as he uses it as well, but is evoked in nearly every future appearance of the Master.