Doubly funny because players might be startled by Ellie's initial attempts at whistling, not realizing it's her and not some monster.
After meeting Bill:
Ellie: We're here because you owe Joel some favors, and you can start by taking these off! (referring to handcuffs dangling from her wrist)
Bill: I owe Joel some favors... is this some kind of joke?
Joel: I'll cut to the chase: I need a car.
Bill: Well, it is a joke. Joel needs a car! Well, if I had one that works, which I sure as hell don't, what makes you think I'd just give it to you? Huh? "Yeah sure, Joel, go ahead, take my car! Take all my food too, while you're at it!
Bill: The tires are rotten and the batteries are dead.
While Bill and Joel load shotguns in the former's armory, Bill notices Ellie touching a pile of magazines (when he explicitly told her in the beginning of the cutscene not to touch anything), resulting in this exchange.
Bill: Hey! What did I say to you when we walked down the steps?! What did I say?!
Ellie reading a joke book filled with the most terrible puns to Joel. He actually groans throughout it.
And then there's one pun that he actually finds pretty funny.
Oh let's not kid ourselves here, most of those puns are gold.
Joel, Ellie, Henry and Sam finding an ice cream truck. When told what it is, Ellie has a hard time believing it.
Ellie: You're totally fucking with me!
After seeing Sam and Ellie play darts, Joel can have a throw too. After much build up, he hits the wall.
After solving a puzzle, Ellie demands a high-five for "Teamwork!" and there's actually a button prompt to do it. Take the prompt for the rare and wondrous sight of a man using his whole body to convey an eyeroll.
Joel's exasperation at Ellie's selection of their horse's name:
Joel: What kind of name is Callus, anyway?
The sniper's log at Eastern Colorado University records people being let in and out. The entry for October 31:
10 million werewolves IN. (Let 'em in just for you, Andrea. Happy Halloween!)
"Once we clean up this mess we're gonna have a town meeting and put his leadership up to vote." The civility of the line in context makes it A Rare Sentence gold. While hunting Ellie one of the cannibals says this about David.
When Joel finds Ellie on the operating table with a surgeon attempting to fend off him with a scalpel, it is possible to throw a brick at his face... only that he ignores the brick entirely, even through it breaks apart on his face.
The... "alternate ending" to the game. The director told Marlene's actress to sing her lines in what was originally the game's final cutscene. Troy Baker took it completely in stride and began to sing with her. See here.
There's a bit of dark humor when Tess and Joel confront Robert after Robert tries to kill them both.