The Shadow Moses heliport with all the flashbacks. Especially the surveillance camera.
I know I first brought this up as a joke nomination for the contest, but I genuinely thought that scene was heartbreaking. Having such an iconic scene just sputter and die like that really underlines how old and obsolete Snake is by this point.
--
"I'm Commander Shepard, and you're standing in the biggest library in Citadel Space. Look me up."