This is probably another instance of me being biased because this was my very first series arc for Doctor Who, but I don’t care. The Bad Wolf is a close second because it was beautifully executed, but the cracks in the universe are still my favorite series-long arc because of how simple they were. The cracks start out as just something for a little girl to be afraid of, but they grow and change into something that can strike fear into even the Doctor’s heart and end the universe. Simple, yet terrifying enough to make a whole fandom fear cracks that they find in things.
Stalking people's LJs, I found a PERFECT post describing Amy and Eleven's relationship from the Doctor's point of view and I liked it so much I want to forever have it on my blog. Worth reading whether or not you ship them romantically or just appreciate their relationship