Agreed with "Genesis of the Daleks." Best Doctor, best villains, decent moral ambiguity and dilemma. Runners-up include "The Sea Devils" (okay, that's purely for visceral enjoyment and the first ever utterance of the phrase "Reverse the polarity of the neutron flow,") "The Pandorica Opens/The Big Bang" (neat ideas and the eps that finally turned around my opinion of Smith,) and the ep "The Doctor's Wife" (some of the finest writing I've seen on TV in a LONG time.)
"You fought with Captain Reynolds in the war?"
"I fought with a lot of people in the war."
"And your husband?"
"I fight with him sometimes, too."