Brennan: I thought you said you'd be down on the next flight.
Booth: I haven't met with the shrink, yet.
Brennan: What shrink?
Booth: Well, the department psychiatrist has to sign a piece of paper saying, you know, that I am not nuts before I get my gun back, so I got an appointment tomorrow.
Brennan: (sarcastically) Great, now I have to break in this Agent Sullivan?
Booth: Sully's a great guy, okay. And for your information, you never broke me in.

Brennan: I understand killers, I just don't know how mothers can do it. I mean, dogs can be trained in a couple of weeks. Kids, mothers have to give up their lives for years.
Booth: No, no. When you're looking at your kid, you don't feel like you're giving up anything.
Brennan: So, you'd do it again?
Booth: What?
Brennan: You'd have Parker, even with everything you're going through?
Booth: What kind of question is that?
Brennan: Wouldn't it be easier if Parker wasn't caught in this drama of yours, with Rebecca, new boyfriend?
Booth: God, no, no, Bones! He's my son. Whatever we're going through, it's not about that and he knows that.
Brennan: That's what parents say when they want to justify themselves.
Booth: You know, I haven't walked out on Parker, alright? I would never have done what your parents did.
Brennan: I didn't say you would, I just - I don't know. You're the father, I don't know anything about raising kids.
Booth: Parker's fine.
(Booth and Brennan in the diner. Booth just finished talking to Parker on the phone)

Brennan: I wish you wouldn't keep letting me hug you when I get scared.
Booth: Hey, I get scared and I'll hug you. We'll call it even.

Brennan: I wouldn't let anyone else call you a loser, Russ. What makes you think you're allowed?
Russ: I love you, too.

Brennan: I'd back down if I were you. He shot a clown once.

Brennan: I'll ask the others but I won't order them. They might have plans.
Booth: It's Friday night and they're racing beetles.
(after Brennan breaks Epps' wrist bone)

Brennan: I'm afraid Angela might quit.
Booth: I'm amazed she stuck it out this long.
Brennan: Why?
Booth: Well, because she's human. I'm sorry, Bones, it's just that, you know, Angela didn't get the same training the rest of you got on Planet Vulcan.

Brennan: I'm not discriminating because he's a Muslim. I find all religions equally irrational!

Brennan: I'm not good playing with toys. What if I can't connect with our child?
Booth: Okay, you connect with me, right?
Brennan: You know I do.
Booth: Okay, our child is half of me, so at the very least, you can connect with the me half. Get it, right? Listen, you're gonna be a great mom.

Brennan: I'm tired of... all of it. I'm tired of dealing with murderers and victims and sadness and pain.
Booth: Bones, it's what we do, all right? We catch the bad people, make the world a better place.
Brennan: No Booth. That's what you do. And somehow I get caught up in it.

Brennan: I've always been proud of you, Zack. I've never met anyone more rational and intelligent. But there's a fault in your logic.
Zack Addy: With all due respect, you aren't cognizant of his logic.
Brennan: Assumption number one: Secret societies exists.
Zack Addy: Accepted. Hodgins has been explaining this to me for years.
Brennan: Assumption number two: The human experience is adversely affected by secret societies.
Zack Addy: Accepted.
Brennan: Assumption number three: Attacking and killing members of secret societies will have ameliorating affect on the human experience.
Zack Addy: Accepted.
Brennan: All of your assumptions are built on a first principle, Zack. To wit, the historical human experience as a whole is more important than a single person's life.
Zack Addy: Yes.
Brennan: Yet, you risked it all so you wouldn't hurt Hodgins.
[Brennan moves closer to Zack and touches her forehead with his as both their eyes tears up.]
Zack Addy: There's... You're correct. There's an inconsistency in my reasoning.
Season 4

Brennan: Is that your costume?
Cam: Uh, yeah.
Brennan: It's sexually alluring.
Cam: Thank you, I'm Catwoman. [Brennan looks at her blankly] The superhero.
Brennan: Oh!
Cam: One of the most powerful female superhero figures.
Brennan: I don't think so.
Cam: Are you kidding? Catwoman?
Brennan: Can you fly?
Cam: I have nine lives.
Brennan: Super strength, super speed, force people to tell the truth?
Cam: I think I'm pretty fast.
Brennan: Pretty fast is not super speed.

Brennan: It took all of my charm--
Booth: All of your charm? Oh boy--
Brennan: Just to get the sheriff to let me look at the skull. When I asked him to let me send the skull to the Jeffersonian, he told me I am not a cop and I don't have any jurisdiction.
Booth: Which is true. Okay, look, what do you want me to do?
Brennan: I want you to get federal on his ass.
Booth: [smiles] Oh!

Brennan: It was an accident. The rib fracture broke off in the fight at the pool hall. [to the bounty hunter] You had no idea that your beanbag gun would kill him.
Booth: Bones, what are you, a defense lawyer now?
Brennan: [quoting Dr. Jude] "A kind mind is a fine mind."
Booth: She cut off his head! That wasn't an accident.
Brennan: I have no rebuttal for that statement.

Brennan: It's a good thing I like being alone.
Booth: You know what, Bones? You're not alone. Okay? Come here.
Brennan: Booth...
Booth: Hey, you're my partner. It's a guy-hug. Take it. [They hug in a very non-guy-hug way.]