In Season Two, an armed man tries to rob a restaurant by holding everyone hostage while escaping convict Benjamin Miles Franklin and his sick daughter are inside. Benjamin, seeing the robber is obviously erratic, manages to control the situation by keeping the gunman and the hostages calm, and tones down the heroics. The gunman decides to hold the restaurant hostage and to wait for the cops, but Franklin appeals to him and tells him, in front of the hostages, that he's a wanted man, and if he goes back to jail, his daughter is going to be left alone. The robber, out of sympathy, lets him and his daughter go, but when it's clear the robber's psyche is deteriorating, Franklin, a trained army man, manages to disarm the man and breaks his arm just as the police arrive. When the police finally come in, though, the grateful civilians in the restaurant had already let Franklin and his daughter out the back door despite knowing he's a wanted man.
In Season Three, young Panamanian prisoner Luis persistently begs known "escape artist" Michael Scofield to let him join a Sona escape attempt he (correctly) guesses has already been planned. Michael continually turns him down for the boy's own safety - life in prison is better than life on the run - but he changes his mind at the last minute. Michael's brother, Lincoln Burrows, then contacts Luis's father and leaves it to him to get his son to safety after Michael's group loses the prison guards. Despite the difficulties of keeping Luis with the group, Michael manages to pull it off, but when they swim underwater to a buoy, the boat that was supposed to pick them up doesn't show up. Eventually, a boat does arrive, but it doesn't respond to their signals, so they think it's the Coast Guard... but it's actually Luis's father, who realized they were taking too long and found out the boat hadn't left the dock yet. This is actually somewhere between Heartwarming Moment and Heartwarming In Hindsight - it's never directly referenced that the group would have died one way or another were it not for Michael's initial act of kindness. (This, of course, is almost immediately followed by another such moment: the surprise party Luis's family throws for him upon his return.)
The plot point may have been an Ass Pull, but Michael's reunion with Sara in the Season 4 premiere definitely qualifies.
Michael's message at the end of "The Final Break", the direct-to-DVD series finale.
Agent Mahone giving the Teddy Bear (which the viewer was led to believe was for his injured son) to Franklin's daughter.
Mahone, Sucre, Michael, Lincoln & Sarah telling Don Self that they won't help him if he doesn't have Brad Bellick's corpse returned to his mother so he can be buried as Self had previously promised to do if anyone died.
Soon after that, there's Michael leaving a police officer's badge on Bellick's corpse after he finds him laid out in his coffin. Bellick had always dreamed of being a police officer, and Michael thought that burying him with a badge was the perfect way to honor him. It's a small gesture, but it shows that Bellick has finally managed to earn Michael's respect and admiration.
This may be a minor one, but the faces and the hug that Micheal and Lincoln exchange after finding one another in "Riots, Drills and the Devil, Part Two show much the brothers truly care for one another
In season two, Sucre is stuck under a log and is urging Michael to leave him. Michael refuses to go anywhere because it would mean Sucre would die.
Sucre: How long you have if you stay? How long until the dogs lead the cops here?