Just a disclaimer, most of these are going to be from Stiles since he is by far the funniest character on the show.
Scott and his mom:
Mrs. McCall: It's not like you're on drugs, right? Scott: Like, right now? Mrs. McCall: "Right now?" Have you ever been on drugs? Scott: Have you? Mrs. McCall: ...Get some sleep.
Stiles and the McCall family baseball bat, from "Pack Mentality"
Stiles: AAAHH!! DO ANY OF YOU EVEN PLAY BASEBALL?
The bat even gets a callback in 3x10 when Stiles brings it to the hospital. Ms. McCall asks about it and it gets lampshaded on it's ineffectiveness.
Which gets another callback in 3x12, when Stiles uses an aluminum bat to prop up the support beam before it falls, and Sheriff says "I told you metal was better than wood."
Jackson's initial assumption that Scott's new found athletic abilities are the result of steroids leads to this confrontation:
Jackson: Where are you getting your juice? Scott: My mother does all the grocery shopping.
Allison's bowling advice, from "Pack Mentality"
Allison: You're thinking too much. You need to put your mind on something else. Think of me... naked.
Which actually works, since it raises his heart rate, allowing his wolf senses to kick in.
And later, during the bowling game:
Allison: Maybe you should stop pretending to suck just for his benefit.
Lydia: Trust me, I do plenty of sucking just for his benefit.
Stiles, on what Scott did while changed.
Stiles: Maybe you caught a rabbit or something.
Scott: And did what?
Stiles: Ate it.
Scott (horrified): Raw?
Stiles: No, you stopped to bake it in a little werewolf oven.
Stiles on his status as a sidekick, from "Pack Mentality"
Stiles: "Why is it starting to feel like you're Batman and I'm Robin? I don't wanna be Robin all the time!"
Scott: "Nobody's Batman and Robin ANY of the time."
Stiles: "Not even some of the time?"
Scott talking big to Jackson:
Scott: "I am great at bowling. (cue Gilligan Cut to the hallway) Stiles: "Scott, you're terrible at bowling!"
Basically, everything between Derek and Stiles during "Magic Bullet."
Stiles: I don't think you should be barking orders with the way you look. In fact, I think that if I wanted to I could probably drag your little werewolf ass into the middle of the road and leave you for dead. Derek: Start the car or I'm going to rip your throat out...with my teeth.
Alison getting her Aunt Kate off Scott's back, by showing her and her dad a condom. The looks on everyone's faces are pretty priceless.
Stiles and Danny:
Stiles: "One more question." Danny: What?! Stiles: "Do you find me attractive?" (Danny remains silent. Stiles leans forward waiting for an answer and falls out of his seat.)
Stiles' voicemail death threats:
I'll kill you. Do you understand me? I'm gonna kill you. And I'm too upset to come up with a witty description about how exactly I'm gonna kill you, but I'm just gonna do it, ok? I'm gonna, grr, goodbye.
Stiles, after identifying wolfsbane before Scott:
Stiles: Haven't you ever seen the Wolfman? Scott: ... No Stiles: *Sighs* You're so unprepared for this.
Derek: You've got to be kidding me. Scott: Was that okay? I mean, it was a howl, right? Stiles: ...yeah, technically. Scott: What did it sound like to you? Stiles: Like a cat being choked to death, Scott.
Stiles introducing Scott to quite a lot of pain and torment in episode six, by use of Lacrosse Balls and a small angry mob. While proceeding to stand there observing things. For SCIENCE!
"Dude! What are you doing to that guy's car?!"
Mrs. McCall: (hears someone enter) Scott? Stiles: (comes through the front door) Stiles. Mrs. McCall: (notices something in his hand) Key. Stiles: Yeah, I, uh, had one made.
Most (If not all) of Derek and Stiles interaction in "Wolf's Bane".
Derek: Oh, and one more thing. (slams Stiles' head into the steering wheel) Stiles: Oh, holy hell, what was that for?! Derek: You know what that was for, now go!
When the sheriff pulls over Allison:
Allison: I'm sorry I was going so fast... Sheriff Stilinski: You weren't going that fast. Just, uh, 75 in a 25, in a construction zone ...
"I told them I'd cut off my one remaining testicle before I'd cut you!"
Scott's quick thinking to get Coach Finstock off his neck at the dance: When the coach sees him there after having told him that he was not allowed to go, Scott quickly grabs Danny and dances with him, making the Coach's Angrish look like homophobia to the rest of the students. Finstock quickly backs off.
Stiles refusing to say "I told you so" in "Formality." Because it's not enough.
The Alpha makes Stiles get into Scott's account.
Alpha: His user name is 'Allison'? *Beat* His password is ALSO 'Allison'? Stiles: Still want him in your pack?
The expression on the Alpha's face afterwards should also count.
Peter's explanation about what will happen if Lydia turns:
Stiles:"Once a month she'll go out of her freakin' mind and try to tear me apart." Peter:"Well actually, considering that she's a woman, twice a month."
Jackson sends a text to Lydia to break up with her early in season 1. She finds him in the hallway and immediately asks if he was trying to be funny:
Jackson: No I wasn't trying to be funny. I would've put a "Haha" at the end of it. And see, there's no "Haha".
Lydia's AWOL and Scott and Stiles think she's turning. They bring this up to Jackson, and...
Scott: We think she's turning. Jackson: Turning... into... Stiles: A unicorn. What do you think, dumbass?
A naked Lydia appears and demands a jacket. Stiles fumbles around, trying to pull off his Dad's, and falls flat on his face. His Dad just rolls his eyes and takes his jacket off.
One of the hunters goes to the police station to kill a new werewolf on the full moon. Derek gets the wolf out of there and leaves Stiles behind with the unconscious hunter and a mess of the jail cells. Enter Stiles's Dad.
Stiles: (beat) Uh, he did it.
Stiles dumping Derek into the water when Derek tells him that he doesn't have the guts to go after the phone. What makes it funnier is that not only did Stiles fail to contact Scott but Derek is not even mad that he did it.
Scott and Stiles chase the kanima into a bar.
Scott: Dude! Everyone in here's a dude! I think we're in a gay club. Stiles: (surrounded by drag queens) Man, nothing gets past those keen werewolf senses, huh Scott?
The entire gay bar sequence until the kanima attack is hilarious in fact. Scott and Stiles attempting to buy some drinks with their ACTUAL IDs, Scott getting sent a drink...
Made funnier by the fact that instead of uncomfortable, Scott looks incredibly proud of himself. Funnier still in that Stiles, who has the Running Gag of wondering if gay guys find him attractive, is openly annoyed that Scott got a drink and he didn't.
Or the exchange afterward between Stiles and his dad:
Sheriff Stilinski: Why are you always at the scene of the crime?! And here, of all places?! Stiles: What, it's a club! We were clubbing! At the club! Sheriff Stilinski: Not exactly your type of club. Stiles: Well, dad, there's a conversation that we- Sheriff Stilinski: You're not gay. Stiles: I could be! Sheriff Stilinski: Not dressed like that.
Which becomes a Call Back when Stiles comments that he invited several friends to get Lydia's party going. Gilligan Cut to several drag queens and their friends at the door. Lydia stares at them for a beat and invites them in.
Ms. McCall desperately trying to act like a serious parent despite her habit of Hands-Off Parenting. She grounds Scott but slowly realizes that its less than practical after attempting to confine him to the house (he has work), take away his TV (it's broken), his computer (he needs it for school) she finally hits on something she can use.
Scott: I need the computer for school Mrs McCall: Then no... uh [sees Stiles waiting in the hallway] no Stiles! Stiles: Wh- No Stiles?! Mrs McCall: [shouting] No Stiles!
In 2x02, the chain falling out of Stiles's locker as everyone turns to stare.
Coach Finstock: Part of me wants to ask, the other part says knowing will be more disturbing than anything I could ever imagine. [turns and walks away]
Stiles, Erica, and Isaac are watching over a drugged Kanima!Jackson in a locked room. All of a sudden, the drugs wear off. Cue a collective and hilarious This Is Gonna Suck look on their faces before they immediately hightail it.
Followed by them desperately holding the door closed, and looking for something to block it with... then the Kanima bursts right through the wall next to them.
The "Sneak Peek" for 2x09 has a brilliant moment. Derek has locked up the baby wolves for the full moon, and they've lost control and are trying with all their might to break free.
Derek: *Completely casual, on the phone* Scott, can you call me back, I'm probably gonna need some help... *Hangs up, looks around at the chaos* DEFINITELY going to need some help..."
This Call Back, but even more so the expressions it elicits.
Stiles is under the influence of wolfsbane punch and is hallucinating, and Scott tries to get him to sober him up but fails. A fellow partygoer tells Scott that she can sober him up. Scott's skeptical, so she proves her point by dunking Stiles into the fountain. Doubles as Mood Whiplash as Stiles's hallucination was a Tear Jerker about his worst fear.
Partygoer: How do you feel? Stiles: Like I'm might have to revisit my policy on hitting a girl. Partygoer: He's sober.
Stiles and Derek have both been paralyzed by the kanima. Derek's managed to get his claws out and digging into his leg in order to kickstart the healing and get the kanima's venom out of his system. When Stiles asks how that's going:
Derek: I can move my toes. Stiles: Dude, I can move MY toes.
Finstock's inspirational speech to the team before the championship game. Melissa and Stiles recognize it from somewhere... and then realize that he's reciting the climactic speech from Independence Day, word for word. The rest of the speech is interspersed with the two snarking about how ridiculous the whole thing is.
While trying to get a Scott and Isaac to bring a cocooned Jackson to them, Peter and Derek finding out about a supposedly evolved Kanima that Jackson may turn into if the situation isn't resolved soon. After the two see an apparently disturbing picture, Peter finds a video.
Derek: He's turning into that? That... has wings. Peter:(small voice) I can see that. [...] Peter: Look, someone actually made an animation of it. Maybe it's less frightening if we... (clicks play, and a disgusting screech emanates from the laptop. Peter immediately slams the laptop shut.) Nope, not at all. We should probably meet them halfway.
Jackson and Lydia in Lydia's car outside the video store, "discussing" what movie to watch.
Jackson:Hoosiers is not only the best basketball movie ever, it's the best sports movie ever made. Lydia: No. Jackson: It's got Gene Hackman and Dennis Hopper! Lydia: No. Jackson: Lydia, I swear to God you're gonna like it. Lydia: No. Jackson: I am not watching The Notebook again! (Gilligan Cut to Jackson inside the store) Jackson: Can somebody help me find The Notebook?
Scott swearing up and down he'll not be distracted from his training:
Scott: If you can teach me [to help defeat the alpha], I can stay away from her. (Gilligan Cut to Allison and Scott making out.)
Scott and Allison both thinking that Stiles is talking about beastiality when he mentions the bestiary.
Stiles: He probably means a bestiary. Scott: A what? Stiles: A bestiary. Scott:(laughs) I think you mean beastiality. Stiles: No, pretty sure I don't. It's like an encyclopedia of mythical creatures. (later) Allison: I think you mean- Stiles: No, I mean bestiary! And the two of you, I don't wanna know what's going on in your heads!
Isaac: Who is this guy? Scott: That's Peter, Derek's uncle. Little while ago he tried to kill us all, then we set him on fire and Derek ripped his throat out. Peter: Hi.
In 2x12, when the group is looking for information on the kanima, Peter pulls something out of a secret compartment in the staircase
Derek What's that? A book? Peter No, its a laptop. What century are you living in?
In the season 3 premiere, Stiles is completely willing to skip the first day of school to look into the deer attack from the previous night. His father suggests begging, bribing, and extorting him to make him leave before literally dragging him out of his room and out of the house.
Scott and Stiles overhears the principal demanding that the damage in the library be cleaned up...and holds up a sword, wondering what the hell it is. So the two quickly book it.
His acidental drop of said condom in Coach Finstock's class.
He distractly putting a glove in the vet office while people are discussing how to put Isaac in a trance.
His interactions with Peter. But especially this:
Stiles: “They’re an Alpha pack, right? So shouldn’t they have a lair?”
Peter: “They’re werewolves not Bond villains.”
Stiles: “Wait a sec. Wait a sec. Maybe they’re living there. You know? Like, maybe the bank vault reminds them of their little wolf dens.”
Peter: “Wolf dens?”
Stiles: “Yeah, wolf dens. Where do you live?”
Peter: “In an underground network of caves hidden deep in the woods.”
Stiles: “Whoa, really?”
Peter: “No, you idiot. I have an apartment downtown.”
Stiles is skeptical that Derek can punch through a wall. He has Derek make a fist, and Derek promptly punches his hand. Scott doesn't know how to react, Peter is dreadfully amused, and Stiles acknowledges Derek can punch through the wall.
Speaking of Peter, Issac and Derek have a discussion which basically amounts to "But I don't like Peter!" "No one likes Peter." Cue Peter coming in and saying he has excellent hearing and that whatever they have to say, they can say to his face, leading to this:
Derek (bluntly): We don't like you. Now shut up and help us.
Those three are made of adorable and funny together. There's also the great scene from the second season finale when Scott and Isaac tell Melissa to zip the body bag around the kanima while it reflexively bites out. Melissa gives a great WTF expression before zipping the bag, while the werewolves back away scared.
Scott: Zip, Mom, zip!
Cora tells Lydia to stay away from Aiden in "Currents".
Lydia: My last boyfriend was a homicidal lizard. I think I can handle a werewolf.
Stiles nicknaming the Ethan and Aidan fusion "Voltron Wolf."
When Peter offers Derek his help in 2x11, he questions:
Derek: Why would I want help from a total psycho? Peter: First off, I'm not a total pyscho. You're the one who slashed my throat wide open, but we're all works in progress right? So......
Also, when Stiles feels like Ethan is threatening him in 3x09...
Stiles: Is he looking at me? Are you threatening me? You know what I'm going to do? I'm going to break off an extra large branch of mountain ash, wrap it in wolfsbane, roll it in mistletoe, and shove it up your freakin- Scott: Stiles, okay!
When Scott gets a tattoo, Stiles is looking around the store while the tattooer prepares himself:
Stiles: Sure you don't want something like this? (shows a picture of a kanima and earns a Disapproving Look) Too soon?
Also from that same episode, when Stiles immediately faints at the sight of Scott getting the tattoo.
Isaac and Derek are discussing the issue of whether or not they should trust Peter (and how they really don't like him), when Peter walks in:
Peter: I hope you're comfortable saying whatever it is that you're feeling to my face... Derek: We don't like you.
In the Overlooked, Chris doesn't know who Jennifer Blake is Isaac declares she's the teacher with the brown hair and that she's "Kinda hot." which earns him a disapproving look from Scott, Allison, Melissa and Chris.
The "Oh, for fuck's sake" face Ms. Blake makes when she looks around her in the elevator—Derek won't let go of her arm, Scott's glaring at her, and Stiles is gripping his bat and shaking as if it's all he can do to not fly at her. Her reaction is hilarious.
The conversations between Stiles and an FBI agent who knows both he and his father (since he's Scott's dad). Stiles, stressed out and not in the mood for this man's interrogation:
Agent McCall: Think you can answer some questions without the usual level of sarcasm?
Stiles: If you can ask the questions without the usual level of stupid.
Isaac's complete irreverence when the FBI is questioning him, Allison, and Scott regarding the missing parents - his parents are dead, after all.
Ethan and Lydia convincing Derek to leave before Kali comes to kill him, and then facing down Kali themselves.
Peter strongly endorses the idea:
Derek: Do you want me to run?
Peter: No. I want you to stay and get slaughtered by an Alpha with a psychotic foot fetish
Lydia does not skimp on the snark, even when confronting a murderous Alpha:
Kali: Who do you think you're talking to? (Close-up shot of Kali's clawed feet)
Lydia: Someone in desperate need of a pedicure. I'd be happy to give you a referral.