In Matt Smith's first season it was the Cracks in Time which was the puzzle. They appeared in every episode and we were told that "Silence Will Fall" the "Pandorica Will Open" etc. Part of the Pandorica/Big Bang episode was the destruction of the Universe and silence (as in no noise) throughout the Universe. Indeed the ending of Vampires of Venice had the Doctor go "shhh" and ask Rory to listen to the silence (no noise). It was fair then to assume when they talked about Silence Will Fall that they meant no noise silence. Instead it's clear now it's showing the unconscious mind, shadow self, as described by the likes of Dr. Freud and spiritual traditions from the millennia. Many aspects of recent Doctor Who has been explicitly exploring this subterranean part of each of us.
In Matt Smith's second season we're learning that the Silence is not about noise but instead about scary creatures who erase themselves from your memory as soon as you turn your attention elsewhere. This Steven Moffatt is one tricky dude, eh?
Last season I went on and on about this theme of the subconscious, how we have a part of us we've forgotten and don't see. This concept was portrayed excellently in The Day of the Moon.
The term subconscious was originated by Dr. Freud but the concept has been taught by spiritual traditions for millenia. It's also known as the Shadow Self, the unconscious, etc. Last seasons episode title, The Beast Below, is a great name for this concept.
It's that this unconscious shadow self is the aspect of our self with a huge influence over our lives, but which we barely pay attention to. Rumbling around beneath our conscious self, the unconscious shadow self squirts its ideas, fears, misconceptions, biases, plans, etc up into our decisions subtly pulling strings to make us think one thing or another thing.
Let's go over how the unconscious shadow self concept is represented in recent Doctor Who episodes.
Having mentioned The Beast Below let's start there. In that case we have a whole society of people being forced to forget that their transportation device is powered by a beast they've strapped to the underbelly of their space ship. Sounds like an allegory for our existing modern society, the source of fuel we use to drive our machines, and how deeply we ignore the inherent unsustainability of this situation.
All through last season we saw how the Crack in Time would erase things from Time and in particular the depth to which Amy forgot her parents, her fiancee, the Daleks and more.
In this season we have The Silence themselves. You see them, then you turn away and they're forgotten. Oh, and they're Silence not as in quiet but as in creatures called The Silence. We don't yet know why they have this name.
These creatures represent the part of us we've deeply forgotten. The part so horrible we don't want to remember.
We've seen several times now a character see them, turn away and totally forget them.
In The Day of the Moon we see Amy wandering around this little girls room. She appears to have a state of shock recognizing that this room is her daughters room, and yet she doesn't remember having this child nor anything about her. A very deep forgetting, eh?
In several scenes a Silence is shown standing in the Oval Office. They're described as being "everywhere" around the world. The Doctor describes them as having shaped and guided human evolution for millennia, and that it's the Silence whose agenda is driving human history.
We know from the Confidential accompanying The Day of the Moon that the voices we heard in the TARDIS last season were The Silence. That in Vampires of Venice, when the fish queen said they were escaping the Silence, it was these creatures they were escaping from. And that they lured the Doctor to Amy perhaps to cause the sequence of events to make his TARDIS blow up the Universe?
"We've heard their voices before in the TARDIS" and "We know they were at the heart of the crack in time of last series." That is, all the cracks were caused by the TARDIS blowing up. Given that Silence creatures had occupied the TARDIS, they caused the TARDIS to blow up thereby causing the universe to blow up.
Curious question is: Why? Why would the Silence want to blow up the universe?
The Silence were first unveiled in: Review: Doctor Who S06E02: The Day of the Moon, Review: Doctor Who S06E01: The Impossible Astronaut