The Human Reaper does indeed bear striking resemblance to a boss from Contra 3. It was a little goofy, but I found the concept of the Reapers reproducing in the form of the dominant species kind of intriguing. Also, that the Reapers determine that humanity is their greatest threat out of any of the sentient races pretty much wholly because of Shepard's actions in the first game.
I completed the game without even noticing the booty call button in my quarters, mostly I'm just pissed that my fish died while I was doing N7 missions. I was so careful with them up until that point, damn it.
As I mentioned in the other thread, I brought Miranda along with me to the final battle (she's really a great character in combat, the combination of Overload and Warp makes her useful against almost any enemy type), and she actually sided with me over the Illusive Man when I decided to blow up the base. Considering that she was both my romance option (I didn't like Jack and I have objections to Tali being a romance at all) and that she was so dyed-in-the-wool loyal to Cerberus at the beginning, I found it extremely gratifying that she resigned and cut off the Illusive Man herself before we got the hell outta dodge.
Along with that, other favorite moments were: Samara's and Tali's loyalty missions, pretty much everything about Mordin, Legion and the new dynamic he adds to the geth, the games salesman on the Citadel, and the turian getting friendzoned by the quarian woman on Illium. Oh, and the part where you play as Joker is pretty great as well.