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- Series creator Kathy Reichs appeared as one of the doctors Zack Addy defended his dissertation to in one episode.
- "The Girl with the Curl" has the Hyperion Hotel.
- Also, Brennan mentions Booth threatening to push someone out a window, possibly a subtle shout out to the pilot episode of Angel, in which Angel (Boreanaz) does exactly that.
- "Boris and Natasha and their Russian Throwing Knives of Death."
- One which is made all the funnier when you realize that Cam has a bit role as River's teacher in Serenity:
Hodgins: Your robot reminds me of you. You tell it to turn, it stops. You tell it to stop, it turns. You ask it to take out the garbage, it watches reruns of Firefly.
- "The Bond in the Boot" is loaded with James Bond references. One of the few that goes unremarked is a CIA front company named "Universal Exports" -- 007's standard cover.
- There are two inside thirty seconds in "The Dwarf in the Dirt" -- "There are no such things as leprechauns" and Homer Simpson's MRI on the X-ray board behind Nigel. Both were put in to coincide with The Simpson's 20th anniversary, a theme running throughout all Fox shows that week.
- Possibly, possibly "Mr. White" in "The Proof in the Pudding." Possibly.
- Booth spends the first half of "The Devil in the Details" dressed uncannily similarly to John Constantine.
- The opening camera zoom during "The Woman in the Sand," set in Las Vegas, is identical to those commonly used on Las Vegas. Given that reruns of both shows air on TNT, once could be forgiven for thinking someone screwed up the scheduling until Brennan starts talking.
- Possibly in the episode "The Death of the Queen Bee", during which Booth and Bones go "undercover" as married to Bone's highschool reunion. Booth is Bobby Kent, newspaper man.
- The episode "The Beaver in the Otter" is one long sequence of references to Animal House, from the title to the Dean being named "Vernon Wormer" and a student having sex with the Dean's wife.
- In the sixth season opener Caroline refers to the Squints as the Scooby Gang.
- In "The Babe in the Bar", the victim of the week is named Harriet. She's a corporate spy.
- "The Maggots in the Meathead" is one big shoutout to Jersey Shore. The "documentary" on the Guidos that Brennan watches is implied to be Jersey Shore itself.
- In the pilot episode, Booth refers to both himself and Bones as "Scully and Mulder".
- Not to mention the episode "The X in the File", which is full of X-Files references and guest stars.
- In the book series, Brennan's mother is named Daisy. On the show, we have the intern Daisy Wick. This is either a dual case of Shown Their Work or just an extreme coincidence.
- The episode title for "The Beautiful Day in the Neighborhood".
- One of the major character interactions in "The Gamer in the Grease" is lifted directly from The King of Kong, right down to the record holder and breaker being named Billy and Steve, respectively.
- In "The Feet on the Beach", one of the employees at the body farm is named Larry Wolfram.
- Hodgins mentions Zack watching reruns of Firefly. No mention is made of the fact that Cam appeared briefly in the beginning of Serenity. Though this might be pretty standard fare for Bones. Mention has been made of watching Buffy by characters, and no one seemed to notice that Booth was on that show for a while.
- There's also an episode where the victim is a spy, whose car and cover story (International Exports) are shout-outs to James Bond. It's Lampshaded by several characters.
- And Star Wars is brought up several times:
Sweets: It's awesome! It's like the Sith Lords, man. There's always only two of them.
Booth: Did you just Star Wars us?
- It's brought up in the first season by Booth, when Zack is wearing the thermal imaging helmet:
Booth: How’s it going there, Darth? See anything on Saturn? (off of Brennan’s look) Oh, please tell me you’ve seen at least one Star Wars movie.
Brennan: When I was seven, and leave Zack alone.