After Frank's run-in with Agent X and Outlaw, Frank is driving off, having stolen their clothes and left them in a phone booth. The "camera" pans to the stolen clothes in the back seat, then pans to Frank wearing Outlaw's hat and listening to country, with a completely serious look on his face.
He's basically a One-Scene Wonder but his appearance in the Civil War was memorable: He joins the Anti-Registration side, enters their base, sees two supervillains, shoots them dead on the spot and is promptly told to leave
Frank is forced to partner up with Daredevil and Spider-Man for The Omega Effect mini-crossover event. The whole time, DD leaves him alone, but Spidey can't stop making jokes. They prepare an ambush, with Spidey leaving Frank to speak with DD and coming back:
Spider-Man: Hey, honey. Miss me? Punisher: I wasn'taimingat you. Spider-Man: Wait, did you just— Punisher: Incoming...
Marvel Knights Series
There are a lot in Welcome Back, Frank but the top one is probably The Punisher punching the polar bear.
During one of his (many) rematches with The Russian, Frank finds himself interrupted by Spider-Man. Unable to fight the Russian toe-to-toe himself, he manages to hold Spidey up in front of him, using him as a shield as the Russian just wails on him. After the fight, as the confused and beaten Spidey regains consciousness...
Spider-Man: Wha... what happen?
Frank: We had a team-up. You were great.
While fighting off the Russian mob from Joan's cottage in the wilderness, Frank accidentally shoots Joan's ducks.
Joan: The ducks! The ducks!
Frank: They had to go.
Pretty much everything the Russian says:
(On first hearing of the Punisher) "Is he like Mighty Thor? I am fan of mighty Thor. He has big hammer, he seems like good Communist..."
(When offered ten million to kill the Punisher) "Ooooh. The Russian could buy many pairs of Levis with that amount. Many compact disks."
The Russian's fight with Frank counts, too. Punching him as soon as soon as he opens the door, smacking Frank in the face with a toilet...it's hilarious.
What about Ma Gnucci leaping out of a burning building without arms or legs and trying to gnaw the Punisher's legs off? That, friends, is determination.
"I am putting ten million dollars on the head of the animal that did this to me." "You—you want us to put a hit on the bear?" "On the Punisher." "Oh."
Castle and O'Brien hooking up in Up is Down.
O'Brien: I've been in jail for eighteen months. When we get through here, you want to go jump in the sack?
Frank: (completely deadpan, with the same face he'd use to make a threat) Sure.
And in Man of Stone.
O'Brien: You cold?
O'Brien: You lonely?
O'Brien: You want to jump my bones anyway?
"Seem to remember telling myself this wasn't going to happen. But that was yesterday."
Later, after they've slaughtered over half of Zhakharov's men, the two of them stand over the carnage -
O'Brein: I'd like to fuck you right here and now, you know that?
MAX!Bullseye is a bottomless well of twisted, dark hilarity. After spending a few issues gushing over how great Frank is, they finally come face to face as Bullseye sits behind bullet-proof glass. After rambling inaudibly to Frank through the glass, he gets out a pen and paper...
Bullseye's notepad: What's your favorite color? Red, right?
[Frank reads, raises an eyebrow and silently pulls out and sticks a chunk of C4 on the glass]
Bullseye's notepad: ...Blue?
During Castle's rampage in Up is Down, Black Is White
Mayor: Well, what's the good news?
Johnathan: Crime's down.
Mayor: Fuck you, Johnathan.
From the Kingpin arc, there's a moment where Frank is heading towards Fisk's home in a car and as he's driving, he notices something...
Caption 1: Funny, could've sworn for a second there was someone following me, in a horse and buggy.