I can't believe I've missed this thread, Doctor Who's become one of my favourite shows within the past 6 months - I love it. I gotta say, I'm with Thuder Peel - 10/Tennant was my favourite. Heck, I'll admit, I was on the verge of crying when I finished 'End of Time' ("I don't want to go").
Now thoughts on stuff:
The 50th/Day of the Doctor - I for the most part loved this episode, it was great to see Tennant back, and I loved the interaction between 10, 11, and War Doctor. My only complaint was that by lingering on the War Doctor's regeneration they gave a brief hope that they had lied, and we'd get to see 9/Eccleston after all. That, and I wish there would have been some kind of interaction between 10 and 11 and Rose - but neither of these are actual beefs.
The Christmas special/Time of the Doctor - really enjoyed it, but was surprised by the regeneration scene - it was pretty quick, I was expecting something bigger I guess (maybe not as long as 10's regeneration (which was not just a farewell to 10, but to everyone from series 1-4/the specials), but still). Don't really have any beef with it though. I'm looking forward to where the show'll go from here.
I also gotta say, series 7 and series 3 are my least favourite. 7, although featuring some great episodes, feels kinda uneven and has the Doctor doing stuff that doesn't make sense for the situation. 3, outside of 3 episodes and the last 20mins of the finale is the weakest to me - I don't much care for Martha, and hated her mother.