Vladimir's death; the poor man has been trapped in space for a long time that he has no idea that he's back on Earth. When Travis defeats him, Vladimir rises up into the sky, spending his last few moments realizing that he was home at last. "Glory to the Soviet Union" indeed.
What comes after is probably the emotional high point of the game.
Travis See that? Now that was a battle! Look at this blood! We humans are alive. Even if we ARE assassins. Doesn't matter if it's a videogame, movie, drama, anime, MANGA, WE'RE ALIVE! People shed blood, and die. This isn't a game! You can't just selfishly use death as your tool. This is Alice's blood. I bet you've already forgotten she exsisted. Same way you would have forgotten about me. And THAT'S why I'm tearing down THE UAA!
The death of Bishop, in retrospect. What was his last thought before getting killed? Travis's name. And of course his death serves as Travis's motivation throughout the game. Despite the fact that he was a borderline sociopath, it shows Travis and Bishop were pretty close.
Ryuji's death. Ryuji falls to his knees and Travis lets out an all mighty scream after finding what was to be his Worthy Opponent. But just as he was about to go to Ryuji, cue Silvia riddling him with bullets. Travis states that Ryuji was a true warrior but Sylvia denies that saying that respect and such would get him killed. As she walks off, we see Travis just bow his head and whisper, "Shit."
Margaret's death. All she wanted was for Travis to memorize her Philistine song. When Travis states he memorized it "100 percent" she dies happily. As Travis walks off, he's whistling the first few notes to Philistine.