John Simm as the Master
Flying aircraft carrier fortress sky island thing
An obvious reset button hanging on the wall
The horde of flying bad guys from another dimension, totally unlike the horde of flying bad guys at the end of season one or the bad guys from another dimension at the end of season two
Anne Widdecombe voting Saxon
"I'm not going to kill him, I'm going to save him"
Prematurely aged Doctor
The Master sending Torchwood to the Himalayas instead of killing them
da-da-da dum da-da-da-dum da-da-da-dum da-da-da-dum ...
Other posts: despotliz here, white_hart here, andrewducker here, iainjclark here, nwhyte's roundup of links here (recursion ahoy!), whatho here, butterfly here, saxonb here, communicator here.