Dan fakes executing Faye; while nothing is the same anymore, he still loves her.
Faye returning to help the team in the final battle, reversing her earlier Face-Heel Turn.
Bo choosing Dan over his orders from Major Philips, if the trust level is high enough.
Cain returning for the final battle, if EVERYONE's trust level is high enough.
Even more moving because no exact explanation is given for that, so it may be interpreted as Cain overcoming the Amada IA's reprogramming thanks to The Power of Friendship.
A subtle one, but after blowing up the satellite dish, while running away through the collapsing building, Dan nearly falls as a walkway collapses under him. It's easy to miss with how fast the scene moves, but looking ahead will see that Charlie - who had been leading the squad out and was the furthest away - was almost all the way back to help you up, before he sees you've climbed back up on your own and keeps going. Really shows how close the squad has gotten.
Also, right before going into the final room to confront the Amada AI, Charlie calls you Dan. Literally the entire game he's only ever referred to you by your rank.