Fallout 3: I was aimlessly wandering the wasteland when I noticed someone running straight towards me. I readied my weapon but instead of attacking the man started talking to me. He told me that he had read the Wasteland Survival Guide and wanted to thank me personally for all the good that I had done by co-authoring it and how much it had made his life better. I continued wandering, head high and spirits soaring, when I noticed some flames off in the distance. Coming closer, I found the source: an enclave soldier wielding a flamer. I dispatched him and his cohorts fairly quickly, then noticed the charred corpses of two ghouls. One was a male, the other a female. Neither was armed. In a sudden, blinding rage, I turned to the body of the officer in charge, stripped her down and unloaded all the remaining flamer fuel into her. I then proceeded to hack off all her limbs and decapitate her, placing her head on top of the nearby comms array as a warning to any others who would come to destroy the peace of the citizens in MY wasteland for the simple fact that they weren't pretty.
Mother 3: I choked up a little at the end of Earthbound when Ness's party defeats Gigyas by calling upon you, the player's, power. I cried like a little girl when, after all that Lucas had gone through, all that I'd helped him through, I was cut off from his world by a black screen giving me the final 'thank you's and farewells from the cast. This game was truly a masterpiece and the most satisfying, loving, and heartrending ending to a series I've ever seen.
Majora's Mask: This one had so many moments; visiting Romani Ranch after "they" came, witnessing Anju and Kafei facing the end together, saving the little girl's father from his curse in Ikana Valley... The hardest for me, though, was the first time I visited Clock Town on the third day (coincidentally because I was doing the Anju and Kafei quest, as well as being the same time I saw the Romani Ranch incident). The bells ringing and the ground rumbling as a constant reminder of how dire things are, the moon taking up the whole sky, the city almost entirely evacuated, everyone left behind in a stupor as they await their deaths, the eerily peaceful music... I had to set the game down and go out for a bit to clear my head after that.