in one of the Christopher Ecclestone episodes a dalek gives a one liner to the doctor: "You would have made a good dalek". That's simply brilliant, in my book, since it opens a whole train of thought on exactly how they differ, and whether it is in fact true. And that, for the thoughtful kind of person, reflects into their own lives about whether they as different from some other group as they assume they are. To me, that is (science) fiction at its best.

I can think of perhaps a dozen such points throughout the series (hmmm, I wonder what the plural of series is?), but I can't think of any since Smith joined.

My favourite 'sight gag' in the Matt Smith era was in "A Good Man Goes To War". Madame Vastra (the Silurian) and Jenny (her 'assistant') have overpowered two guards and one of the guards (picking up on the chemistry between the two) says "I don't know what she sees in her", at which Madame Vastra lashes out at the guard with her six-foot tongue.
Fortunately it will have been completely lost on the kids!