Looking at that list it's bloody hard, because there's been so many brilliant episodes during this era. When the 11th Doctor era hit, it bloody hit good.
I can just never tire of watching the Eleventh Hour; it remains, for me, the perfect way to introduce a new Doctor (and era) seamlessly. Everything just works, from the writing to the performances... Matt had me sold on his Doctor pretty much from day 1, after thinking his intro in the End of Time seemed very Tennant with an added "geronimo."
I also really enjoy the Angels two parter; it's interesting watching those, remembering they were the first episodes Matt filmed as the Doctor, and seeing just how much he nails it. I will always have a special place for the series 5 final; I just love the personal nature of it all; no matter how serious and massive things get, at the end of the day it's all about the Doctor's relationship with Amy, and what he's prepared to do for her.
In fact, I think as a whole series 5 is the strongest series of the show, but 6 and 7 have some stronger episodes.
Impossible Astronaut/Day of the Moon was a revelation; I could barley believe this was the same show that it had been under RTD (no disrespect intended, as I love RTD). It was just so grand in its scale, had an immensely shocking opener; I think this is probably where the 11th Doctor era really peaked for me.
Well, obviously, it goes without saying the Doctor's Wife is sublime.
I'm a massive fan of AGMGTW, mainly because I always like the episodes that show the Doctor in a new light. Here, the Doctor is showing just how dangerous he can be; easily summoning an army of people to help him decimate the Silence. Then there's Lets Kill Hitler, which I think is a fun episode and finally provides pay off about River Song. TWORS, I thought at the time, was such an awesome way of paying off the Doctor's "death" from the start of the series; when I watched it (in a crowded pub, long story) I had a massive smile on my face and was proper hyped for what was to come.
Series 7 was such a step down that very few episodes in there contend for my favourite. Bells of St John and Name of the Doctor are probably the two best, but special mention to Nightmare in Silver. I wouldn't say any of these are my favourites, but they easily stand out in series 7.
The Day of the Doctor is, imho, superb. It's the best possible anniversary special I think they could have given us without trying to bring back everyone who's ever been in Doctor Who and making it a mess. It was a tightly constructed story entirely focused on the Doctor, with more than enough nods to the show's long history.
The Time of the Doctor I enjoyed, but enjoy less every time I see it. It's OK, but the Silence pay off throws up a few big questions that lead me to believe this was not Moff's original intention (if he ever even had one!), and I think Matt deserved better really.
In all... I think I have to go with the Day of the Doctor. But it's a very difficult decision.