There are sooo many funny quotes from Stargate Atlantis so narrowing them down was hard! I have many more than this, but here are some of my favorites:
Sheppard: You seem nervous.
McKay: No, I'm part of this team. I'm doing this.
Sheppard: Yes, you are. I just said you seem nervous.
McKay: Oh, really? I thought you said 'Rodney, you don't have to do this.'
McKay: Maybe we should offer a sense of humor in trade…
Sheppard: Sure…they can have yours.
McKay: (laughing) Ah, hahaha, oh, please my side… you slay me.
Sheppard: On second thought...
Weir: The city can handle that?
McKay: Yes. Theoretically.
Sheppard: Like 'dinosaurs turned into birds' theoretically or 'theory of relativity' theoretically?
McKay (looks confused): What? Um, somewhere between.
McKay: (explaining to Sheppard why he has to take the farthest grounding stations) I need to get done quickly so I can start working on the subroutines, and Elizabeth was complaining about her knee the other day so...
Sheppard: Wait, whoa, w-wait a second. Are these things even close to a transporter?
McKay: Uh, yes, Elizabeth's is.
Sheppard: And mine?
McKay: Uh, it's a brisk walk away.
Sheppard: And by 'brisk' you mean... far?
McKay: And, by 'walk' I mean 'run'.
(McKay get distracted while flying the Puddle Jumper)
Sheppard: Don't let go of the controls!
McKay: Snapping doesn't help!
Sheppard: This is why parents get someone else to teach their kids how to drive.
McKay: I'm both insulted and touched by that.
Beckett: You have a date, Rodney? With a woman?
McKay: It is simply two adults sharing some friendly...Yes, with a woman!
Sheppard: All right, stay close and stay quiet.
(He looks at McKay)
McKay: Why does he say that to me?
Sheppard: McKay, stay here and help Beckett.
McKay: Medical research is really not my thing.
Sheppard: And hunting the Wraith?
McKay: I meant I could stay and help Beckett.
McKay: See how I almost stunned that guy?
Sheppard: I must have missed it.
McKay: Yeah, but if he was, like, a step to the right, I would’ve stunned him for sure.
Sheppard: Good for you!
(after Rodney was shot in the butt with an arrow)
McKay: You know, you really don’t appreciate the simple things in life, like sitting.
Sheppard: I don’t envy you. Must be a real pain in the ass.
McKay: Oh, how long did you work on that?
Sheppard: Longer then I care to admit.
McKay: It's that look. That's the same look I get when I have a brilliant idea.
Sheppard: How would you know how you looked?
McKay: Cause it's happened more than once in front of a mirror, ok?
McKay: It's complicated. Look, imagine them as leaky pipes okay?
McKay: So you pump water through them, they leak right?
Sheppard: Dumb this down any more, you're gonna get hit.
McKay: We gotta go back.
Jeannie: Go back? Why?
McKay: Because I got all mixed around. We gotta start again. Maybe what I thought was north was south. It's hard to tell.
Jeannie: I can not believe I am betting my life on your sense of direction.
McKay: What are you talking about? I have an excellent sense of direction.
Jeannie: Oh really? Remember when we went to West Edmonton Mall and Dad had to call the police to find you.
McKay: That mall is huge!
Jeannie: There are maps every 7 meters!
McKay: Misleading ones!
McKay: (to Sheppard) We're about even when it comes to looks, right?
Sheppard: Who's been lying to you?
McKay: No, I'm being serious.
Sheppard: I am too. Who's been lying to you?
(Sheppard, McKay and Harmony are in a cave when they hear the screams of Genii soldiers)
McKay: What the hell was that?
Sheppard: The Genii just had a little run-in with the beast. (to Harmony) Alright, be a brave girl and stay here with McKay.
McKay: Hey, hey, hey. How come I always get stuck as the babysitter?
Sheppard: You wanna check out the beast?
McKay: No. I'm good here.
Sheppard: Thought so.
Keller: Woah woah woah, wait wait, don't pull me up!
McKay: What?! Why?
Keller: I see light!
McKay: No no no no no! Don't go toward the light! You want to stay in the land of the living!