During the Seoul mission in Chaos Theory, the player is required to call in an airstrike on a downed jet to prevent North Koreans getting some important data aboard it. The player is then told to leave the pilots to die in the blast rather than make several incredibly risky trips past a tank and a few soldiers; saving them, however, prompts Sam to say some pretty heartwarming stuff:
In the final level in the sixth-gen version of Double Agent, if you interrogate the terrorist in the room where the sprinklers go off, this conversation takes place.
Terrorist: So... You're gonna kill me? Sam: Let's have a little chat and see if it's necessary. Terrorist: Forget it, I ain't selling my guys out! Sam: They'd be happy to rat on you. Terrorist: That's their call, not mine. You kill me, I go to heaven with my conscience clean. Sam: That must be nice for you. (When interrogated again) Terrorist: For what you're gonna do, son, I forgive you.
At Conviction's White Box Labs, Sam rescues a scientist from the Black Arrow mercs. The scientist explains what's going on, and lets Sam into the elevator. Sam tells him to get out, and the guy says he'll hang around, because his friends might need him. He's willing to face take on armed, elite mercenaries for his coworkers. And maybe because he knows they've been working on a weapon. Or both. Doesn't really matter.
Sam finally reuniting with his daughter in Conviction. After all the crap he's been put through over the course of Double Agent and Conviction, seeing him hug his daughter brings a smile to your face.
The aftermath of Tom Reed's demise in the Oval office. Despite being played as bitter sweet, Sam has fought off the full might of his old employer, the largest PMC in the USA, prevented an Day of the Jackboot and is finally home with the person he loves and is ready to start a new life.
This little dialogue at the end of Conviction:
Victor Coste: He talked about learning who was really important to you, and why you always had to come back for them. He talked about family. And you know what the last thing he said to me was, just before he hung up? "Vic," he said, "Thanks for everything. I love you like a brother." Brother. That's family right?
In Blacklist, the various calls to Sarah. Optional, but they show that while he's gotten back into the espionage business and has taken a level of Jerk Ass due to Vic's injuries, Sam still tries his best to be a good father.
Grim gets a major one. Near the climax of Blacklist, she calls out Sam on his Jerk Ass attitude to the team and basically tells him to show some more respect to them. This reduces the friction between the team members as Sam had already alienated Briggs and Charlie.
From the first game Sam tries to call his daughter Sara, "This is Fisher... I mean dad."
Blacklist: When you end phone calls to Sarah you can hear just a hint of conviction's main theme. This may be pretty minor, but it reminded me of how great it was for Sam to be reunited with his daughter.