2. Claras Sickbed and Clever Clocks
Okay, again, Im cheating. These moments are both endearing for the same reason, but they were both just so lovely I couldnt resist. So lay off me, imaginary-accusatory-staring-people! When Clara has just died and come back (again), the Doctor takes her upstairs and tucks her into bed. But he doesnt just do thathe goes manic and makes up a whole sickbed for her. He runs around getting a glass of water, a vase of flowers, and some biscuits. Sure, he eats one of the biscuitsbut notice that, when Clara wakes up, thats how she knows shes not alone. The whole thing shows how much he cares about Clara, and how happy he is to have found her.
So does the other moment classified under Clara. The Doctor paces about, trying to figure out what Mrs. Gillyflowers plan in The Crimson Horror is. Clara tries to stop him twice to tell him the answer, until she actually has to physically hold him still.
Then the Doctor gets this smile, and calls her Clever Clocks. She answers with Miss me? And he mutters Yeah, lots.
And you know from his delivery that he really, really means it.