Some of these may have been mentioned, but I think ME3 deserves some positive feedback as well, so I'll say them anyway.
Having a shooting contest with Garrus (I've always thought of Garrus as Shepard's (both male and female) best friend, and this was a great moment)
Mordin - Every scene with him made me both sad and happy, and the ending of his arc was incredibly well done.
NOT A DEFENSE OF THE ENDINGS BUT The little scene of Anderson's Last moments with Shepard on the citadel. The music, scenery, and writing were spot on.
The final misson on tuchanka - This was featured in one of the early trailers, and if anything was actually more epic in the actual game. Kudos to the giant pissed off thresher maw.
The Music - Seriously, the new compositions, the synthesis (no pun intended) of old songs and new, and occasional callbacks to previous themes were just so. damn. awesome. (by the way, I mean the eddie izzard interpretation of awesome, go look it up if you don't know what I'm on about)
The romances- Other than the fact that we didn't get as much of Miranda as I was hoping, the rest of them were handled very well.
I really hope the ending business gets wrapped up to everyone's satisfaction, because despite all the criticisms leveled at them, there's a reason we still buy Bioware games: nobody else does it the way they do.