One moment from before the game actually released: One of the Kickstarter stretch goals was to include an extra mission in the game which tied the story back to the SNES and Genesis Shadowrun games. This mission was to be included only for backers of the project. However, after getting a bunch of backer feedback, Harebrained Schemes elected to make the bonus mission available to everyone and not just backers. The community wanted the mission shared with everyone, even if they did not contribute to the Kickstarter.
Dead Man's Switch
Potentially, the Player Character in Dead Man's Switch. Sam was there when a run turned sour years ago, and now he's set things up so that if someone offs him, you're the one he goes to post-mortem for help. Even as the investigation spirals out of control into something much bigger than anyone anticipated, and various motivations pop up along the way, you have the choice to do it just to keep faith with an old friend who always had your back. Even when the payoff from Sam's life insurance turns out to be just another one of his cons, you can brush it off with a shrug because it was still the right thing to do.
Coyote's reunion with her brother, albeit bittersweet, evokes the warm and fuzzies from the description after he's talked down.
He drops the gun and Paco quickly scoops it up. Coyote grabs him fiercely. He slumps into her arms and she rocks with him for a long time, her head buried in his shoulder. When she looks up, she locks eyes with you, the deepest gratitude reflecting on her face.
This ending also gets her to stop her crusade against BTL dealers - if he dies, she goes into den after den for revenge against the types of people that took her brother away from her.
From the Dragonfall Campaign: Players who already know of the eventual fate of the Flux State might believe it to be pointless to donate to Samuel Beckenbauer's charity, since it's possible that Samuel will be unable to keep his properties; that's not the case. If the player helps Samuel reach his final goal (purchasing the larger building and turning it into a civic center), the building he purchases is able to stand up to the assault of the mercenaries who attack the Kreuzbasar, something which saves the lives of many of its residents when they take shelter in it; the building he used to house his charities in would not have been able to do so.
For that matter, practically any of the positive changes the player effects in the Kreuzbasar. Getting Kim off of her BTL's takes the cake, though.
Comforting Dante after Monika's death, persuading Marta to save the kids and turn against Harrow, and trusting Dietrich's nephew to make the right choice by himself are all awesomely heartwarming.
The Atonement or Good Fortune endings, provided you took your time getting to know your team and the nicer residents of Heoi, are rather sweet. You're able to walk around and see how the residents weathered the coming storm, the Ka Fais potentially see you as the saviour of their family, and talk to Matthew and Ambrose and Crafty. Then there's the team, from Racter asking you to witness the future he'll create to reflecting on your successes with Gaichû to sharing a quiet hotpot with Gobbet. The Good Fortune ending adds an extra dose of fuzzy to it by having Raymond around, allowing you and Duncan a chance to catch/make up with him.
If the player prompts Crafty Xu to continue her mother's research, she eventually realised that her mother essentially died for her work. While Crafty still resents the fact that her mother valued work over family, she managed to forgive her mother.