17. The Girl Who Waited (S6, E10 2011)
Past episodes of Doctor Who have given us insight into the lives of Companions, and some of them have even shown them on massive undertakings on their own. (The Last of the Time Lords, part II of Series 3's two part finale, had then companion Martha Jones roaming the Earth to spread the gospel of the incapacitated/incarcerated Doctor.) But it wasn't until The Girl Who Waited that we were presented with a true Companion-centric story. Due to a fluke on a diseased planet, Amy is trapped in a separate, faster moving time stream. This causes a time expansion inequality that causes her to age much faster than The Doctor and Rory's subjective point in time, and puts them in the room with a decades older Amy. The ensuing temporal complications set up what is both one of the most touching episodes of Doctor Who in its modern run, and also a very effective commentary on what influence The Doctor has on his companions.
18. Closing Time (S6, E12 2011)
Continuing the Craig storyline was probably one of the best decisions made when it comes to the modern era. What makes Closing Time essential though is the story's ability to go on a separate Doctor and Craig adventure and tie it directly into the overarching story for Series 6. Through the one off plot of Closing Time, we find out what life is like for Amy and Rory outside of The TARDIS; and we also encounter the ultimate set up for the finale of the series' arc involving The Doctor's murder. More importantly, we're given more of The Doctor leading a normal human life and giving us a lot to laugh about, much like he did in The Lodger. However, it's tempered with a sense of the end drawing near. By the end of the episode, The Doctor has confronted the fact that he's running from his impending doom, and he's embraced his fate. What happens next is the follow-on to a setup that we've been promised would be resolved all season.