In the MAX series story The Long, Cold Dark, there's Castle caring for his infant daughter whom he wasn't aware of until recently.
At the end of that arc, as Frank is giving his daughter away to O'Brien's sister he shares a moment of when he and O'Brien were in Afghanistan and he saw O'Brien watching the sunrise, with a small, content smile on her face.
Frank: Memories like that I like to kill, but you can do something with it if you wish.
Frank retrieves a bottle of rare vodka in Russia and leaves it at a Brighton Beach bar for a Russian WWII vet to drink.
From the same arc, Punisher says that Nick Fury sent him in not for the biological superweapon, but to rescue Galina, the little girl. Fury agrees, considering he sent the one man who could do the job and not kill the kid. He then states he'd have gone personally, but he needed to watch the generals, lamenting he did a poor job of it.
Frank leaving his neighbors (and the first friends he has had in years) with a large pile of the mob's money, with a note telling Joan to use it to move away from a city that scares her.
I may be damned, but I'm not going to drag you good people down with me.
Frank helping out Daredevil in The Devil, Inside And Out counts (see the CMOA page for more details). Especially this exchange:
Matt: "I never thought I'd say these words but... Thanks, Frank."
Frank: "Not necessary. You're hurtin' a lot right now, Murdock, with good reason. But you don't want to be me. You needed to remember that"
This is especially notable since Daredevil is the superhero who is the most determined to put a stop to the Punisher.
That arc deserves special mention. Upon seeing a newspaper article that Murdock is in prison, Frank immediately walks up to a thug (in plain sight of the police), shoots him, puts down his gun, and turns himself into the police. All so that he can go to prison and help protect Daredevil.
Don't know if this really counts but in Kitchen Irish, the moment when the gangsters decide to put an end to all the bloodshed and open the old Nesbitt treasure together, made me feel warm and fuzzy inside.
In one issue, Punisher and Spider-Man team up to rescue several persons at the Daily Bugle (Mary Jane among them) from a hostage situation; however, their differing views on Thou Shalt Not Kill result in the two acting separately. At the end of the story, the hostages are rescued, the bad guys are caught, and Frank happens to stumble across an unmasked Spidey (who he only sees from behind) having a tender moment with Mary Jane. Seeing this, Frank leaves quietly.
In the almost unbearingly bleak Punisher MAX story arc "The Slavers" Frank launches an assault on a group of human sex traffickers by first drugging their food to knock them out so he can take out the bad guys without harming the sex slaves, but one of the girls passes out face down in her stew and suffocates. It's a small scene in a very bleak story, but seeing Frank calmly and gently cleaning the girl's face, his inner monologue "I figured I'd cross this bridge when I came to it. But nothing came." brought a lump to my throat.
In the very last issue of Punisher MAX after Frank's death Nick Fury is sitting in a bar, in low spirits about how little lasting impact Frank actually had on the city. Cue him seeing a news report of numerous vigilante uprisings and an image of several people wearing tributes to the Punisher (skull facepaint, skull mask, etc). Fury notes that Frank got his rightful eulogy. The next and final panel being the Castle family grave with a new tombstone featuring Frank's name alongside his family. Doubles as a Crowning Moment of Awesome.
Thomas Jane and Ron Perlman made a fan video during work on The Punisher film. They, as much as Garth Ennis, gave Frank his balls back. The kicker is the ending, the girl who was assaulted was left the lighter and the kid being picked on gets to keep the t shirt that was dropped, only to open it up to see the skull. His reaction says it all, "Holy shit that was the fucking Punisher."
A similar scene occurs at the end of the slavers arc in the game. After planting bombs on the ship and speeding away with several of the girls Frank hands one of them a detonator, letting her blow her captors sky high.
The three part graphic novel series "Punisher and Captain America: Blood & Glory" features the two teaming up against a criminal conspiracy that tricked Frank into trying to assassinate Captain America. The series explores the dynamic between the two, highlighting that they're two very different soldiers from two very differentwars. At the end when the two are about to go their separate ways, Frank gives Steve a Vietnam Combat Infantry Badge, something given only to people who served in the conflict. Frank tells him that he should've been there with them—because they needed good men like him watching their backs. As Frank walks away, Steve calls out after him, addressing him as "Captain Castle". Frank turns around to see Steve giving him a salute, which Frank returns.
In that silent moment, there are no "super heroes". No sanctioned patriot and hunted vigilante. We are only soldiers fighting the same fight for the country we both hold so dear. Each of us but one among equals.
In Punisher: War Zone, Frank's mercy killing of the reformed gangbanger Carlos. Having earlier denied that a criminal could reform...