Here are my favorite moments from the modern Doctor Who, in no particular order.
Sarah Jane: "It's you!" - Sarah Jane's reunion with the Doctor after thirty years was so perfect. I really don't have much to say about it.
The Tenth and Eleventh Doctors joining the War Doctor to fire the Moment - While the 50th anniversary special (in my mind, this phrase is always said in the sarcastic voice of Moffat's secretary in "The Five(-ish) Doctors Reboot") had many awesome scenes, this one is the best. The older Doctors finally come to terms with the way they ended Time War and join together to support their earlier self and repeat the action, tacitly admitting that it had been and still was the right thing to do. I tear up every time I watch this, and I've seen this episode at least 25 times. While the rest of the episode was great fun, to me, this is where the story should have ended.
Donna joining the Doctor to set off Pompeii - The Doctor's life and responsibilities are not simple, black and white moral choices. Donna learns that and steps up to support him, as best friends do.
Donna punching the Doctor on the arm - Do you even know which scene I'm talking about here? When Luke Rattigan takes the Doctor's place and destroys the Sontarans, the Doctor survives and appears back on Earth. Relieved that he's still alive, Martha runs up to hug him, but Donna punches him on the arm, earning her a very surprised and offended look from her target. The moment doesn't even last a second, but it tells you everything you need to know about their relationship.
Ninth Doctor's regeneration - This regeneration fit the incarnation and his relationship with Rose perfectly. 'Nuff said.
The Doctor in the stasis chamber - The Doctor is trying to fight off the solar entity from taking him over, and he's terrified. Moreover, what he's terrified of is not his impending death/regeneration, but that he's not going to be able to stop himself from killing everyone on the ship. The Doctor is never more the Doctor than at this moment.
"Everybody lives!" - The sheer joy in this scene, from the weary, cynical alien, is breathtaking.
Playing football - This is very meta, but I really love watching Matt Smith (who wanted to be a professional football player) play football.
The Doctor in the window - Which window, you ask? Kazran Sardick's. This scene, where you see through the video record that the Doctor has gone back in time to change Kazran's past to try to fix the present, was beautifully done. (Of course, he's broken the Laws of Time, but Eleven does that many times and will do so again later in the same episode, so we can overlook it here.)
The Doctor in the window - Yes, there's another window. This time it's Reinette's. This episode is beautiful all the way through, but the moment that does it for me is when the Doctor realizes that he's thrown everything away to save Reinette and is stuck on the wrong end of time.
"He never raised his voice..." - The fate of the Family of Blood. Terrifying, cruel... Just gorgeous.
"So much bigger on the inside..." - Everything about the TARDIS' interactions with the Doctor while she was human (Humanoid? We really don't know if Idris was human, do we?) was perfect, but my favorite moment was when she realized that these sentients had so much more in them than you can see from the outside.
