This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Bravest Warriors
The Emotion Lord. With great power, comes great insanity, indeed, and worse yet, he seems pretty aware of the fact that he's a complete loony and there's nothing he can do about it. Is he really the jolly old loon who knows more than he lets on?
He's also Chris from the future, can't forget about that!
Your best friend is suffering from a horrific disease and a basket case is impeding all hope of treatment.
"The Parasox Pub" Makes it about ten times worse, showing Chris An entire pub full of Emotion Lords, all insane due to not ending up with Beth, and all determined to get Chris to kill an innocent man to get them free, all willing to destroy spacetime to fix their own past.
Impossibear's antics in Gas Powered Stick provide a stark contrast to Chris and the Emotion Lord's latest schemes. The scene where Plum spoils the Emotion Lord's plans (or does she?) is unnerving, especially when she glares at him.
Plum has two brains. Just seeing it for the first time is unsettling.
Ultra Wankershim. The Emotion Lord grants Chris a vision of the future. It's... not pretty.
The Cereal Master. What kind of abusive, horrific childhood would cause such disturbing, self-destructive acts? And more importantly, what kind of father would do that to his own child?
RoboChris. Basically, a robotic skull with Glowing Eyes of Doom and Chris's hair and a simulacrum of his personality. The scene where RoboChris sneaks into Danny's room in the middle of the night is extremely unnerving...though it's subverted somewhat when instead of killing Danny, RoboChris attempts to seduce him with a sexy dance.
Hamster Priest is hilarious as it is horrifying. Watching Beth's reactions to Chris being killed via being thrown out the airlock, everything and everyone she knows and loves twist and shift in nightmarish ways, and her PoV as she's killed by being thrown out the airlock is nothing short of disturbing and heart-wrenching.
Ralph Waldo Picklechips is building the Worm a new legion of followers. He's also summoned the Worm into the Bravest Warriors' dimension by using his own daughter's brain waves.
Danny's pain and suffering in Mexican Touchdown is hilarious in its audacity and because he's doing it all in a misguided attempt to impress Plum, but the prisoners of the alien pound, less so. Imagine being mind-controlled by an evil alien artefact that fills you with indescribable joy for all of five minutes, followed by untold hours of sheer, soul-crushing depression. Your tears are used to feed your captor, meaning you are trapped in there till you literally cry yourself to death.
Jelly Kid Forever has Danny's breakdown over Jelly Kid's death. The Psycho homage scene is terrifying, more so to anyone who has watched that movie.
Not to mention Catbug killing Jelly Kid to begin with. If you think of the two as just pets, it's upsetting, but not so horrific, but the team's pets are treated as equals. Catbug basically murdered Jelly Kid.