Kisses after his operation in "Stan's Best Friend"...He went from being the cutest dog ever to everyone's nightmare for the next few weeks as soon as you see him...
Stan's eating disorder in "The American Dad After School Special". When we finally see how skinny he really is... it isn't pretty.
Stan: I know! I'm a huge tub of lard!
What's worse is that this is how anorexics see themselves in real life. No matter how horrifically skinny they get, their minds will always see themselves as fat and they'll work on being skinny, even if it kills them (which it will). The episode actually won a Prism Award for showing anorexia nervosa in a realistic light (and showing that eating disorders aren't just something insecure girls and women get; insecure men and boys can get them too).
And people with eating disorders will sometimes have a Jerk Ass imaginary "friend" who represents their ED thoughts, and he/she does tell them they are useless, fat, need to stop eating, etc.
Stan getting both his legs bitten off by a polar bear in "You Debt Your Life".
Barry's criminal mind when he doesn't take his medication,
The gruesome remains of the rat from "Season's Beatings"note The Christmas episode from season seven where Stan gets kicked out of Christianity after footage of him beating up Roger dressed as Jesus and calling him a "lazy, wine-loving bisexual" makes the news and upsets every Christian denomination in the world, while Hayley and Jeff adopt a little boy who turns out to be the spawn of Satan, and is the result of Roger trying to make his ideal spiked eggnog. He gives a sip of it to the brown rat, which takes effect after a beat. It squeaking like a banshee while clawing at its head for a few seconds, then rips the black rat's head off and makes out with it, before putting it on it's head like a hat and running a couple laps around the cage in a frenzy, before finally pausing to vomit up a fountain of blood and keel over dead. Then its chest explodes.
A scene from "Toy Whorey" where Stan and Steve meet a guy who uses hand puppets as the prostitutes for his whorehouse (think Mitch Connor). One of the puppets has human teeth and tongues (and are later seen vomiting).
Roger cutting off Jeff's skin and grafting it onto his own in "Love, American Dad Style". Worse, Roger nearly did the same thing to Hayley out of love.
Roger: The hat's keeping it all together.
Roger surprising Hayley with Christina Aguilera's severed larynx.
And Roger using it like a whistle with Aguilera's voice actually coming out of it.
The Lady Bugs from "Not Particularly Desperate Housewives" never got any mention? They were this close to killing Francine by ramming shopping carts into her, had Linda Memari not stepped in.
In "Tears of a Clooney", Stan handcuffs Francine to a radiator so she won't go out and kill George Clooney. Francine escapes by cutting her own hand off.
In "Tearjerker", the title villain (played by Roger) creates a film so sad, that it literally makes people die crying. Roger than shows Stan and Sexpun (Francine) the results of the critics' screening, with their dead, pale, teary-eyed bodies.
Her Nightmare Sequence from the beginning, where a school-aged Hayley gets in trouble for not coloring an American flag in the lines, symbolizing how everyone wants her to conform. The worst part? It wasn't a dream.
Stan, Francine and Jesus getting buried alive by the Antichrist in Rapture's Delight. They're only trapped for a few seconds, but the fact that Francine's scream gets drowned out to silence as they're buried is rather chilling.
In "Fartbreak Hotel", Francine's Imagine Spot when she stabs Roger, decapitates Stan with a butcher knife, and chases down Steve and snaps his neck.
Stan's presentation on why above ground sprinklers are bad in "Roy Rogers McFreely" consists of showing a crude cartoon that depicts a little girl falling on and being impaled by a sprinkler, which shoots blood into her friend's face.
A scene from "National Treasure 4: Baby Franny: She's Doing Well: The Hole Story" where Henri Watkin sees his wife again...and bites off her nose.
Made worse when you realize why he likely did it. He probably had a lot of pent-up aggression towards her, since we don't get any indication that she attempted to send rescue for him or simply have his body recovered. Imagine spending over 40 years trapped underground and realising that the person you love has left you to rot in a well?!
In the episode "Naked to the Limit, One More Time". Roger throws Jeff into the UFO's beam that was meant to take Roger back to his planet, we're pretty sure we'll never hear much of him again...
We do, though the fate of those abducted by Roger's people is scary they are kept as slaves on the shopping mall-style gigantic spaceship, (which itself isn't really that scary). Now your free to go, as long as you pass the love test; a test that proves the alien abduction separated you from your true love. If you fail, you get castrated and it's rigged for you to fail.
It's no surprise either to find out that this brutal punishment is also Roger's fault, for cheating on Emperor Zing and breaking his heart.
While the actual reason why Stan doesn't want to enter a bike race with Steve is a lot better, the story he tells about his friend getting hit by a train and having pieces of the bike lodged into his organs seems a little . . . unnecessary.
"The Boring Identity" has Stan, Bullock and others killing workers at Doug and Buster's in painful and gory ways.
In the episode Hurricane!, the family gets caught inside their house, now upside down, during a flood. The scary part is when a shark swims into their house and gores Hayley. Throughout the rest of the episode, they are menaced by the beast and can never tell when it will surface and attack.
Klaus' decaying human body in the episode Da Flippity Flop. And later, he steals Stan's body.
Klaus' situation altogether. His human body was lost and he's been trapped in the body of a goldfish for decades, simply because the CIA didn't want him winning a gold medal for East Germany in the 1986 Winter Olympics. Even if he wasn't apparently a nice guy before getting turned into a fish, he still didn't deserve that awful fate.
"Moon Over Isla Island": the dictator Juanito tripping over the upwards escalator after choking a corn dog, which in addition to killing him, leaves his body disfigured.
Also Harsher in Hindsight due to the (natural) death of Ricardo Montalban a few months later, making this his final role.
When Stan visits Roger's mind in "Brains Brains and Automobiles", a bird lays an egg on the boat that hatches into a Klaus fish with Steve's glasses and Hayley's hair. It then makes a horrible screeching sound.
The mutant clone mix of Steve's girlfriend Glitter and Stan's dodo Darren from the end of "Steve and Snot's Test-Tubular Adventure".
Francine accidentally slitting Steve's throat at the end of "Office Spaceman".
The ghost of Francine's unsatisfied dead sex drive from "Poltergasm". Specifically, the demonic face on Roger's surveillance camera.
Roger:(recording) 3:43...Just pissed myself.
Klaus' Sanity Slippage over being stuck in his hotel room with a broken back in Atlantic City with the hotel guide menu on a constant loop with the remote out of reach.
Steve's "war flashback" from "In Country...Club", which is depicted in an Art Shift to a more realistic style, where a soldier is graphically split in half by a helicopter blade.
Stan's transformation into a woman from "Stan Goes on the Pill".
"Blood Crieth Unto Heaven" is rather creepy and mostly based on the atmosphere and lacks many actual jokes the show might normally have.
In the most recent episode "The Longest Distance Relationship" Jeff and Sinbad find a wormhole that takes them back to earth and so returns so he can return to Hayley. However the wormhole takes Jeff 60 years into the future. He is still reunited with Hayley and gets to see what happened to all the Smiths in the future. Francine has had loads of plastic surgery to look young still but looks horrifying. This was most likely intentional.