Honorable Mention: In the first Armored Core game on the original Playstation, one of my earliest missions was in a tunnel where I had to protect this tanker truck from terrorists. The opening briefing was the most well-delivered line of dialogue ever: "Raven, the tank is full of explosive gas, so please be careful." The actress who said it sounded truly heartfelt and it actually made me feel guilty when I blew up the tanker on accident.
Runner-Up: Amy Rose and E-102 Gamma's respective storylines in Sonic Adventure for Dreamcast. Gamma is a really underrated character in the Sonic universe, and his dialogue with Amy aboard Eggman's airship is perfect. It's truly sad that level of brilliance was never reached by the later Sonic games.
Defining Moment: Zone of the Enders 2: The 2nd Runner. Toward the end, Ken's frame is disabled, and you have to carry her up through various levels as a flood rises up toward you. Occasionally you have to put her down to fight off a few enemies, then frantically pick her back up and make your escape. It's no exaggeration when I call that sequence 'transcendant'; it's kind of a perfect damsel-in-distress scenario, albeit Ken is no wilting lilly and Dingo's not exactly Flash Gordon. At the risk of sounding like a complete and utter cornball, I felt like a hero, and being a complete coward in real life, that was pretty special.