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 ScoobyGang.
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.
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 a pretty major character there 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.