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I'm not sure the Doctor and Sec ever really counted as friends. Sure, Sec redeemed himself at the end of the episode, but he they didn't go for ice cream together, and the human-Dalek hybrids in the same story, or Caan in "Journey's End", were at least friendly as Sec was.

The three prototype humanised Daleks in "The Evil of the Daleks", on the other hand, might actually count as friends. The Doctor gave them names, they played choo-choo trains with him, and they couldn't wait to run around and tell all the other Daleks about their exciting new friend. And he seemed to genuinely like them as much as they liked him, even if Jamie was a little suspicious.

He was friendly to Oswin in "Asylum of the Daleks" even after finding out she had been converted into a dalek.