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 getting into fights in prison, Frank immediately walks up to a a pimp beating a prostitute near a policeman. Frank casually cracks the pimp's neck, tells the prostitute to clean up and get out of the business, and turns himself into the police. All so that he can go to prison and help protect Daredevil.
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.
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."
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 Civil War, Punisher joins Captain America's Anti-Registration side, and is an accepted member right until he guns down in cold blood two supervillains who try to join them. Cap immediately begins beating him half to death, demanding why Punisher won't fight back: Not against you."◊
The 2005 videogame:
After planting bombs on the ship and speeding away with several of the girls Frank has just rescued from slavers, he hands one of them a detonator, letting her blow her captors sky high.