I know we're only for episodes in, but this has been an eventful opening to the season. If you're not caught up on your viewing yet then tread carefully, spoilers lay ahead. It also may get a bit long.
In the first fifteen minutes of the series opener, "The Impossible Astronaut," the Doctor gets killed and then killed again in the midst of his regeneration rendering him completely dead. Though we find out that it's the Doctor from 200 years in his own future the two part premiere fails to prevent/explain who kills him and why he dies. I also think the little sequence from the beginning of the Doctor leaving Amy and Rory messages throughout history may prove important.
Clearly the build up to his death or the prevention of his death is going to be an overall arch of the series. As is Amy's phantom pregnancy. With the presence of two Doctors and a woman who is simultaneously pregnant and not pregnant, I can only assume there is some sort of duel timeline or undecided reality taking place. I believe this has something to do with the Silence (or Silents-- grammatical ambiguity in their name).
Amy's pregnancy (to me) seems to be a plot of the Silence. The Silence tells her to tell the Doctor 'what she must not tell him,' and when they capture her they say, "We do you honor, you will bring the Silence." Amy is also being followed by a strange woman in a metal eye-patch that makes comments to her or about her and seems to exist in another layer or dimension.
In this week's episode, "The Doctor's Wife" we see a physical manifestation of the TARDIS (who thinks Rory is pretty). It was an interesting study on the relationship between the Doctor and the TARDIS and asks who exactly stole who away from Galifrey. Though it seems to stand by itself in the series arch, there are two points to raise. The first is that since the Doctor is so attached to the TARDIS and it is sentient and has some choice in where it lands, why is the future Doctor from "The Impossible Astronaut" without TARDIS?
In the end, Idris with the TARDIS in her tells Rory "The only water in the forest is the river." I'm wildly curious about that. It seems to be an obvious allusion to River Song, but forest and especially water imagery keeps coming up in the show and has since the mid-Ten years.
One final thing that has caught the attention of several Who-bloggers are the messages encoded on the BBC Doctor Who page. In the section on the site "The Fourth Dimension" there are facts about The current episode. In those facts are italicised words. When you line up all the words in italics it forms these sentences:
Ep. 1: "All the secrets you seek can be found here on the Webb."
Ep. 2: "We found your message! You're alive! But what secrets 'D'you mean my friend?"
Ep. 3: "I mean I glimpsed him! And may the gods help him. Perhaps you can."
Ep. 4: "To see what I saw, click on the spot beyond the Doctor's home planet."
It seems to be a conversation between two people. After this week's message you can click the period or "spot" after the word "Galifrey" (the Doctor's home planet) and it links to this video entitled "Analysis Lessons." Make of it what you will.