I really loved The Impossible Planet two-parter. It's the only time in the current series that the Doctor has faced a god-like adversary. Some of the best episodes in the whole series have that (Pyramids of Mars, The Celestial Toymaker, um, The Three Doctors).
Welcome spoiler for series three: the Daleks are in it, but fortunately it's not a world-ending finale and just a "normal" story.
I really hated that they turned up in Army of Ghosts. That was an utterly superb Cyberman story until the Daleks breezed in and it became obvious that Russell T Davies preferred them.
Loved the condescending banter between them at one point though.
"Daleks do not take orders!"
"You have identified as Daleks." D'oh!
Series 3 and 4 are even better and certainly the strongest two so far.