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 première definitely qualifies.