These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Acceptable Targets: Wiccans in "The Witch in the Wardrobe", BDSM practitioners, LARPers,...
Environmentalist they are shown to be amoral assholes who regularly cheat on their spouses and feel that because they are doing more for the earth they have the right to do whatever they want regardless of how everyone else feels.
Alas, Poor Scrappy:The death of Dr. Nigel-Murray. Just when you thought you could deal with him...
Zack Addy. Partially through season 4 he reveals that his killing of the lobbyist was only Metaphorically True, and he hadn't eaten human flesh. Making Zach's only crime being an accessory to murder.
Pelant surviving Boom, Headshot. Booth's bullet manages to miss his brain stem and all other vital bits, going out through his right cheek. The worst injury he suffers from this is a discolored and blinded (but otherwise intact) right eye and maybe some missing teeth, the rest being just scarring from where he stitched his face back together. It's clear the writers saved him for the sole purpose of dangling him over the team's heads for yet another season. They finally offed him early in Season 9, so it's likely he just lived to give them a reason to hold off the wedding.
Badass Decay: In the first couple of seasons Brennan is presented as a capable and skilled martial artist. This seems to have been abandoned in later seasons, noticeable in "Harbingers in the Fountain" where an untrained doctor clumsily wielding a simple scalpel is more than a match for her.
In Season 7's "The Warrior in the Wuss", she provides some significant information about Karate, and just about any self-defense instructor will tell a student that just because someone is untrained doesn't mean they're not a significant threat, especially if they're armed and/or highly motivated. Even in the first episode, she was perfectly willing to shoot a guy threatening to burn both of them to death instead of trying to subdue him.
She's back to taking out three guys at once in the season 6 opening.
The Gravedigger, whose victims are buried alive. And we learn that the motive amounts to "because I can".
Howard Epps. It's not known exactly how many women he killed, but we know of six. He manipulated Bones and her True Companions into stopping his execution, and then escaped prison by starting a fire and killing a fire-fighter, dressing in the man's uniform, and walking out, only to continue his twisted little mind games with Bones. He shows up in her apartment, tries to kill her, and jumps from the balcony, killing himself by letting go of Booth's hand.
After Hodgins and Angela broke up, he got Hodgins drunk and gave him a tattoo of Angela.
He insisted that Hodgins and Angela had to name their daughter Staccato Mamba.
When Hodgins refused, he got Hodgins drunk and gave him a tattoo of himself (imagine having a tattoo of your wife on one shoulder and her father on the other), as a way of congratulating him on standing up to his father in law.
Creator's Pet: Pelant. Hated by fans, check. The writers really seem to enjoy writing him. He's put into major scenes for no reason (other than being a Diabolus Ex Machina), and shilled by other characters, who are very quick to call him brilliant and even say that he's smarter than them. Ultimately, however, the writers made the right call and finally ended him.
Critical Research Failure: In "The Twist in the Twister," it's clear little to no research was done on severe storms. To start with, when a body is discovered to have been deposited by a tornado, the investigators completely neglect to check the path and rating of the tornado. Worse, the storm chasers themselves are grossly incompetent, with their leader stating that a mesocyclone in an already developed supercell is only just forming, when in fact a tornado is mere moments away from touching down. One character—who happens to be in the third trimester of pregnancy at the time—drives into the tornado and makes it without a scratch because she didn't touch the funnel itself. Finally, minor debris strewn across unmoved and otherwise unhurt vehicles leads the storm chasers to conclude that the tornado was at least an EF 4. Oh, and how does one get a full rainbow against a clear blue sky instead of a retreating thunderstorm, anyway?
Possibly a case of Reality Is Unrealistic, in the episode The Bullet in the Brain, Bones mentions that Booth holds the world record for longest confirmed sniper kill at around a kilometer(she says it was slightly less, he says it was more). In real life, there have been no less than ten confirmed sniper kills at more than a kilometer, several at twice that range, and every one of them was made years before the episode aired.
Crosses the Line Twice: Billy Gibbons (Angela's father) forcing Hodgins to get a tattoo of her and then leaving him in the middle of the desert. Good thing he lived. And this is after promising Angela that he won't seek revenge. And then he does it again, this time because Hodgins refuses to let him name the baby something ridiculous.
Gratuitous Special Effects: A particularly egregious example occurs in at the end of an episode where Bones and Booth start shooting nerf guns at each other. The balls are clearly CGI and the actors are clearly pumping empty guns, and it rather begs the question why not just use real nerf balls and save the special effects budget?
Harsher in Hindsight: During Zack's security interview in "The Woman in the Car," the interviewer asks him if he would divulge government secrets if logically persuaded. He replies that he would never do so without asking Brennan first.
Hollywood Homely: The Wiccans in "The Witch in the Wardrobe". Booth is repelled at seeing them naked during their ceremony but when we see them clearly in the light of day all of them are at least slightly above-average lookswise.
Zack and Vincent seem a bit like a bickering couple in Booth's coma dream.
Sweets and Vincent share a very, ehem, interesting glance at the end of "The Babe in the Bar".
Idiot Plot: Pretty much the entire Pelant arc requires the team to be complete morons in order to work. For one thing, the team discover that Pelant can hack anything with a net connection, so what do they do? They leave the cameras, Angela's computer, and everything else the way it is. Then they leave their bank accounts untouched so Pelant can steal all their money instead of withdrawing everything they have and closing their accounts. This is just the tip of the iceberg as to the idiotic things the team has to do to keep this villain from being shot dead within 2 episodes.
Internet Backdraft: The Season 8 finale has ignited a firestorm of rage over what many have called an outright Diabolus Ex Machina aimed right at Brennan and Booth's relationship for the sole purpose of generating melodrama and making Pelant into a Villain Sue.
Moral Event Horizon: Arguably, killing a random woman because she was in the way was this for Broadsky. Killing serial killers made him vaguely sympathetic, in a Max Keenan sort of way, but this seemed to cross the line. Of course, Caroline disagrees:
Caroline: Man sneaks into [Booth's] house, threatens [Booth] with a gun. That's unforgivable. He should be lethally injected just for that.
Sweets allowing Brennan to think Booth is dead for 2 weeks for reasons that basically amount to For Science! is considered to be an unforgivable act by much of the fanbase, to the point of turning Sweets into The Scrappy for many.
Epps' various murders and sick games are bad enough, but when he saws his wife's head off while she's ALIVE, it's pretty clear how evil he is.
Not to mention sending her heart to Angela (after reading that she was called the "Heart of the Operations" by Hodgins) and booby trapping the head of his wife with a glass capsule containing a highly poisonous powder, which almost killed Cam.
Narm: The birth of Booth and Brennan's baby. Slow-motion in a manger.
The writers kind of realized this and joked during the Paley Center interview that they thought about giving Hart Hanson, his wife, and son a walk-on part at the end of the birth scene as the "Wisemann" family.
"I don't know what that means." Bones having No Social Skills is one thing, but her using that same exact phrase every single time someone makes a pop culture reference got old extremely fast.
When Robert Englund shows up as a high school janitor who had a thing for knives and death you figured he was the killer. Nope! Nice guy all along.
Played very straight with French Stewart playing a bit role as a fundamental preacher who gets shooed away by the cops in the beginning of the episode. He wasn't even in the running until The Reveal (by the characters, at least).
Paranoia Fuel: Pelant's computer voodoo is this in-universe. Imagine a sociopath who has complete control of any electronics and can track you no matter where you go unless you go completely off-grid, and even then he might try to hack a satellite or your car's GPS. If you get on his short list, he WILL find you, and God only knows what your fate will be. Granted, out-of-universe it becomes severe Narm to most viewers, but Pelant's mere presence in DC at the start of season 8 caused Hodgins to force everyone to forgo any form of computer electronics for the entire investigation, due to the fear of Pelant hacking them again and sabotaging the entire operation.
The Gormogon. "He's very fast, and very strong..."
Also, what the Gravedigger does to victims.
There was one episode where they realized the victim had been stabbed in the neck. That didn't kill them. It just mostly-paralyzed them so that when they were buried alive in concrete, they tried to swim to the surface with only their little finger.
"The Princess and the Pear". Guess what the "pear" is. And a version is made for use further south. If it's any comfort to folks, Pears of Anguish don't actually work — they're psychological torture as the force needed to use them on either location is more than a Pear could exert. The Pear would break long before the human would.
"The Critic in The Cabernet". Red wine. Body. How do you think they discover it? ...EWWWW! The liquefied man was somewhere between this and Nightmare Fuel.
Then there's the flattened girl who is often being compared to a pizza. They even use a piece of sheet metal to pry her off the cardboard she's stuck to. Thanks a lot.
Then there's the person that was in used fry batter stuff... it's the usual, right? Bones says that it's not her department and walks off... and then, when they pull the body out, the skin starts falling off, the organs start slipping out, and Bones quickly returns, since it is now in her department.
"The Babe in the Bar": an episode with a person who drowned in the mold of a giant chocolate bar. All of the decomposition gasses were trapped in her body and liquified it. Also, they didn't find the body until after the bar was set and they had begun cutting it. Cue liquidy goo spewing out of the giant candy. Imagine if they had started eating it before they found her?
"The Bullet in the Brain": Aside from the Gravedigger's head exploding and seeing her headless body, there's also the woman's body half-dissolved in lye, that Brennan and Booth find. Both of them immediately start retching. Keep in mind that they have been working together for about five years by this point, and Brennan has identified remains from mass genocide graves.
Booth's handiwork on Pelant's face hits the trifecta of Squick, Body Horror, and Eye Scream: the right side of his face got completely blown open from the inside, and the right eye looks like some sort of cheap glass eye, completely blind and useless. Pelant had to triangle-stitch the wound without any anesthetic, and even after healing, the scars are still VERY visible. It would've been nice if Booth had killed him with that shot, but seeing Pelant's Plot Armor finally crack was still impressive.
Angela: Can you imagine what it was like for her, waiting and wondering, never knowing what happened? Bones: I don't have to imagine.
The season three finale still makes my eyes water.
And let's not forget to mention when Cam adopts Michelle that one moment when she goes up to her room to get the salt shaker.
Booth and Brennan sharing "scars" from their childhoods as a way to comfort Sweets after discovering whip scars on his back.
"The Superhero in the Alley," when Angela completes the victim's comic book for him.
Bones tearfully telling Booth that she can't let go of her relationship doubts despite how she feels about him.
"The Finger in the Nest". Poor Hodgins. Poor Sweets. Poor Brennan. Hell, this episode is one Tear Jerker after another. Particularly if you're a dog lover.
The sixth season premiere, "The Mastadon in the Room", in a good way when Hodgins and Angela are talking about their baby.
"The Doctor in the Photo" brings out Brennan's oft overlooked woobie side. Her tearful breakdown and confession to Booth at the end is especially emotional.
"I'm with someone now and she's not a consolation prize."
As a man who has been on the tail end of a rejected marriage proposal what happens to Booth at the end of "The Daredevil in the Mold" is particularly jarring.
"The Shallow in the Deep", when Angela gives faces to all of the slave ship victims.
"The Blackout in the Blizzard". TJ Thyne can make the chemical composition of coins bring tears to your eyes.
The death of Mr. Nigel-Murray, especially when Cam talks about calling his mother.
When the squints realize that Zack is Gormogon's apprentice. When Bones pressed her forehead against Zack's and he started crying, this troper burst into tears.
It may have been badly written, but the actors still completely sell the scene of Booth cancelling his engagement with Bones. Brennan looks utterly devastated, and Booth is torn somewhere between outward anguish for wounding the love of his life, and highly internalized rage directed at himself and Pelant.
A physicist who regretted being a distant father eulogizes his gymnast daughter the only way he knows how, with calculations of the ways she moved through life — crawling, walking, running, tumbling — until
Bones: She is at rest again.
With bonus awesome for Bones, who used logic to talk the guy out of committing suicide (basically, if he killed himself the cops would think he was guilty and stop looking for other suspects).
The Unfair Sex/Double Standard: While the show is feminist and portrays a wide range of strong female and male characters, it will occasionally veer into this category generalizing men as Acceptable Targets, whereas you do not dare do the same to women.
For example, in "Yanks in the U.K., part 2":
Hodgins: I thought women loved it when we fought over them Cam: "Women" is an unacceptable generalization. (10 minutes later) Angela: Men are stupid.
Or in "The Finger in the Nest"
Bones: Pitting animals is a common pastime in evolving cultures where violence is more commonplace and animal life has no value. Angela: To men. Bones:Yes, it's always men.
Trolling Creator: Executive Producer Stephan Nathan seemed to really be enjoying how much the fans wanted to kill him for the season 8 finale. His response to being told dropping Pelant like a nuke on the B&B engagement was "not right" was to laugh and call it "so much fun to do."
Villain Sue: As of the Season 8 finale, Christopher Pelant, in spades. Thankfully, Season 9 starts with Booth making an absolute joke out of him and blowing him away.
The Woobie: Sweets and, to a lesser extent, Zack. And if you don't feel bad for Hodgins during season 4, there's something wrong with you. Heck, Brennan herself-underneath that Insufferable Genius exterior lies a very vulnerable, fragile soul-the times when it's exposed tend to quite sad.