I'm trying to think back to The Pandorica Opens (my Doctor Who DVD collection is missing most of the revival's box sets), when all the Doctor's enemies united to stop him from destroying the universe. I know Daleks were in that mix.
Under Moffat, the Daleks have undergone a subtle metamorphasis. Keep in mind, I was never much impressed with the Daleks. One of the few things from Tom Baker's Doctor that I liked was his admonition, as he climbed into an air duct, "Well, why don't you climb up here and get me?" Harry Dresden commented on the uselessness of zombies, "What good is an army that moves slowly and keeps moaning about brains?" Likewise, I was never much impressed with an invading army that could be defeated by a staircase. IIRC, it was during Sylvester McCoy's run that the Daleks finally developed a levitation ability to overcome this (although it was to them what Float is to Flight in City Of Heroes).
With the revival, the Daleks are actually becoming scary to me. There are so many out there, and only one individual, the Doctor, actively working against them. The Cybermen are only interested in survival. As long as you don't have anything they need, you leave them alone, they leave you alone. The Daleks are out to conquer everything. And they no longer have just the Zerg Rush going for them. They now have puppets (including one who looks an awful lot like the next companion coming up when Amy and Rory leave at Christmas. Ooo, foreshadowing!) that, unless you are paying strict attention, you would never guess. Now, that happens to you, you're dead, your body is simply being used as a host. Very Body Snatchers. It's the fact that the Daleks can convert a human into a Dalek that really freaks me out. It's the lynchpin of Evil Of The Daleks (Season 5, Patrick Troughton), but hasn't been touched on since and used the "old" origin of the Daleks.
In many ways, the Daleks are very much in the vein of the evil brain creatures from sci-fi B movies. Whereas zombies were the loss of free will, the loss of the mind and your body becomes someone else's plaything, evil brains were the loss of the human heart, the emotions that temper our worst actions (Donovan's Brain, The Brain From Planet Auros, etc.). They became a shorthand for logic and rational thought running unchecked to their conclusions. The Daleks eschew any emotion other than hatred, probably because it is the only one they cannot give up. Without their self-defined superiority and their technology, they are weak mutations who have difficulty surviving without the artificial ways around their natural limitations. I wonder if some Daleks secretly hate themselves, aware of how contradictory their existence is.
I also wonder if the Doctor regrets Genesis Of The Daleks. The Time Lords sent him to stop the Daleks right at the beginning, and he couldn't bring himself to do it. That means the Time War, the genocide of the Time Lords that he triggered, everything is entirely on him. And the Daleks have only gotten smarter, as with the WWII episode.
Each season has a running theme going through it, starting with Bad Wolf in the first. Last year, with Amy's Schrodenger pregnancy, you had the themes of red and blue to denote the events (even reflected in the Doctor's tie. During the first appearance of the weeping angels, I almost immediately figured there were two different Doctors running around. A friend of mine thought this was bullshit until he rewatched the episode and saw the "second" Doctor approach Amy from the opposite direction he just left in. But his tie also changed color, which sealed the deal for me).
This year, it's all about memories. Remembering. This has been there all through time, with Amy restoring everything, remembering Rory, and so on. But this one episode pushed it up. Begging the Doctor to "remember her". The Doctor escaping because the Daleks didn't remember him anymore. Oh, they will soon, don't worry -- not only is there enough info on the Doctor out there (the web site from the first episode Rose) that they'll know if not remember their Predator, but Oswin still remembered him even after she wiped him from the neural net. It only lasted long enough for him to escape (the Doctor still took a stupid risk. Once I had teleported inside the safety of the TARDIS, you wouldn't have seen my ass for dust. Instead, the Doctor not only lets them know he landed inside, he actually steps outside to confront them despite the risk of everyone opening fire on him. At least, he didn't reveal Rory and Amy made it. Hopefully, the Daleks think they snuffed it when the blew the asylum to bits).
With the whole thing about replacing love with hate and conversion from one thing to another, not to mention the Daleks finding the Doctor's hatred "beautiful", I think Moffat is leading to a point where the Daleks attempt to convert the Doctor, adding his positive qualities to make them completely unstoppable. The Doctor is not on the run to save his life, but to remain himself instead of being turned into a component of the Daleks.
Each year has upped the danger the Doctor is in, from being the means for the Time Lords to return and wipe out humanity to the Pandorica to being murdered. Each threat is a great fear of the Doctor's writ large. And now, the Doctor is at risk of becoming what he hates.
Just like we all are in our own ways.