The end of the Captain Vladimir boss fight. At the end of the fight when his visor is broken open he can finally see the Earth, which he hadn't even seen in years while isolated in that suit. We see it from his eyes and see his aged face gazing into the sky in his final moments, as his ship ascends. Many Manly Tears were probably shed.
Travis: It's over, Captain.
Vladimir: This is... Earth?
Travis: Yep. Welcome home.
"Glory to the Soviet Union".
Margaret's end of the fight can also work. Margaret isn't angry at her death... In fact the last words she says to Travis was whether or not he memorized her song. When Travis replies that he did, she answers that it was "so...sublime", then dies. When Travis is walking off, he whistles the first few notes to 'Philistine', honoring Margaret's last request for him.
Travis: I won't forget... Alice.
Henry returns in a Big Damn Heroes moment and decides to kill all of Jasper's lackeys for Travis. How does Travis respond? With a small smile and a "Thanks, bro."
There's The Stinger. It's the resolution to the recurring scenes in the phone room, and Travis reunites with Sylvia. She's very happy to see him.
Shinobu returns to the series with a less dire attitude, cocky and even a little playful. She sees Travis as her master (trainer, not owner) and incorrectly throws out some of his phrases (mostly moe) in the most adorkable ways imaginable.