Season 4 Episode 3 The Finger in the Nest The dog is part of an illegal dog fighting ring and his master commanded him to kill someone. Because of this, the dog is put down.

In season 1 episode 4, the first scene shows a dead bear laying flat on its back, with a woman examining the contents of its open stomach

Season 4, Episode 3 focuses on an illegal dog-fighting ring, so features discussion of dogs being abused and neglected, but all of that happens offscreen and no dogs are abused on-screen.

Yes there is bugs in most episodes they are normally seen in with the character Jack

Season 8 Episode 4 they find the remains of a Tiger that was killed shortly before they arrived.

Yes, they're used as a torture method in season 3 episode 5 The Mummy In The Maze especially

In one of the cases, Cam is pressured to cut into a head, a powder comes out and causes her to have a seizure

It's a show that's murder-oriented, and sadly there's visuals of torture too, including that one^

Trigger warning In almost all the episodes, the bones examined by the doctors are cracked, dented, snapped or fractured in some way

On a few occasions one of the main characters, Booth, sees ghosts, however it is unclear if the ghosts are real or due to a brain injury that is revealed later in the series.

Yes in 'Mummy in the Maze' episode there is a clown with a gun

In season 2, Bones's father continues to contact her and in some cases follow her or come into her apartment despite her asking him to stop

One of the cases, Bones makes someone vomit because they swallowed evidence but you can see it coming because fingers go down his throat. Also a science guy for children comes in and he vomits quite early in the episode

*spoiler* In season 9, Wendell Bray (a squintern) is diagnosed with Ewings-Sarcoma after Dr. Brennan looks at his x-rays after he broke his arm. He, after some debate, decides to go through chemo. He ultimately survives.

One of the main characters gets sent to a mental institution, (he's fine though) and there's some scenes in it.

Someone cuts her hand to find out if a man has vasovagal syncope

Many of the main characters are socially uncomfortable enough to react with panic to occasional extreme social/professional situations, and footage of crime victims and perpetrators often features panic and anxiety reactions.

There is an episode I recall with a child pageant where the murdered child is said fo have refused food/etc. I recall several other mentions of eating disorders, but usually they are not explicitly shown.

In season 10 episode 17, the death is ruled to be a suicide staged to look like a murder and the dialogue discussing suicide after can be incredibly triggering for many people who have dealt with suicide. They do not speak badly of depressed and suicidal people, but they talk about hopelessness in a way that many find uncomfortable.

Season 2; Episode 9: "Aliens in a Spaceship" -- two characters are essentially buried alive

S08e09 is shown almost entirely from the POV of the victim's skull that the team takes to carrying around because some of them believe that the boy's soul is still there. The picture is sometime shakey due to this

No, but in the final episode there's a while where they don't know if the baby inside Angela is still alive

Several characters give birth during the series, three of those happen more-or-less onscreen. SPOILERS:: the most explicit one is when Bones gives birth in s07e07. Her upperbody is shown throughout as well as her legs and the freshly born baby. Angela gives birth in s06e23 in a hospital, she is shown several time during labor and her upper body is shown during delivery but it is clean. The freshly born baby is shown. Daisy gives birth in s10e08. She is shown several times during labor and her cries can be heard during delivery

The episode features transphobic jokes from several of the main characters, and doesn't take much care about the language they use, but overall the episode's tone is very positive - the transphobes in the episode are depicted as criminals and villains. Booth makes one transphobic comment, to which someone responds, "Don't say she 'used to be' a man, that makes you sound ignorant." Thereafter, when the rest of the team is having trouble with the victim's pronouns, Booth asserts firmly, "From now on, 'he' is always 'she'. She was a she when she died, so she deserves the respect due to him or her... okay, person!" While this is not the most "optimal" way to be an ally, Booth unmistakably is one, and the overall tone of the episode attempts to be respectful.

In s04e07 the victim is a transgender woman who is at first identified as male based on her skeleton. Her wife (who she was married to before she came out or transitioned) refuses to acknowledge her identity. Booth purposefully misgenders her several times while interrogating suspects to manipulate them (either to placate them, or to get a rise out of them). The majority of the main cast as well as the people in the victim's life re supportive. In s04e23 one of the people assisting on the case "identifies with a subset of an urban Japanese aesthetic known as kei [...] It glorifies androgyny", but the squints spend the episode trying to guess their "real gender". At the end of the episode Angela hugs them and later tells the squints that they are a guy. In s09e23 the victim is a drag queen and there are several drag queens interviewed during the investigation. There are a few instances that might qualify as misgendering and also where Booth deliberately does t to get a rise out of someone

there is a secret n**i in one of the episodes

Though most episodes end happy, some don't although the series overall has a positive ending.

In a few cases they find people hanging i know s1e3 does

Season 2, Episode 8: "The Woman in the Sand" -- underground fight rings in Vegas

SPOILERS There is a character that Booth and Brennan tried to save but couldn't, and he fell to his death. He deserved it though.

Not nuclear but many explosions

There is a long running arc with a killer who burries people alive. There is an entire episode set inside a car that has been buried with it's occupants still alive. The show continues to talk about the trauma caused by the events even after they occur.

Several victims and in s02e09 Hodgins is hit by a car but survives