The monster that comes out of the dimensional portal in "Deedeementional". It's a giant pink blob... thing with a VERY fang-lined mouth and a disturbing roar. And for its first on-screen action, it sprinkles salt on Dexter, devours him, and you can actually see little amoeba things in its stomach begin to digest him.
As for the episode itself, it ends on the horrific implication that Dexter's plan to send Dee Dee into the past to prevent him from opening the portal is doomed to fail.
To explain: after Dee Dee is sent back in time, she tries deliver the message to Dexter, who aggressively rebukes her, causing Dee Dee to run off in tears to be comforted... by herself. Then Dexter, realizing that Dee Dee wan't lying about her time traveling, he tries to get the message from her, only for both Dee Dees to jerk him around and withhold the message until Dexter, fed up, decides to try and trick them into entering the portal. Guess what happens next. And then, when Dexter gives them the new message, only then does Past!Dee Dee give him her message, causing Dexter to realize that he is, quite in fact, "doomed". And then, while repeating the "This had better be important, woman." bit, the episode ends on the ominous shot of Dexter's notes and blueprint of the portal.
One episode, "Filet of Soul", started off with Dexter and Dee Dee's pet fish dying and Dee Dee refusing to let it get flushed down the toilet. Later, the ghost of said fish comes back to haunt them because he was denied entry to "the sewer beyond". The ending parodied the classic ending from the "Thriller" music video.
And if that's not enough, there's the part where a giant tentacle comes out of the toilet and grabs Dee-Dee.
The episode "Jeepers Creepers, Where is Peepers?" featured Dexter and Dee Dee's magical friend Koosie working together to save Peepers (another magical being) from an anime villain, in one scene we see a rather disturbing graphic look at Peepers as he is having his energy sucked off. HE'S INSIDE OUT.
And this line from Peepers in a voice that is equally disturbing as the scene mentioned above: "Help me, Koosie, help me." *shudder*
There was also the episode "Dream Machine" (3rd segment). The title alone pretty much sets you up for an entire episode based around Nightmare Fuel. The worst part is the ending, in which Dexter suddenly comes to a realization that he's living in a nightmare because Dee Dee is smarter than him, at which point his clothes come off and he ends up stark naked in the middle of a laughing crowd. (Said crowd turns into a very creepy Eldritch Abomination a moment later.) Afterwards, he gets taunted by a bunch of laughing Dee Dees and the episode ends with him falling endlessly, screaming for Dee Dee to wake him up, but she happens to be asleep.
What about the episode with all the clones in it? At the end due to the overuse of the cloning machine, There is a creepy fusion of Dexter, Dee-Dee, and her two friends, that talks in a weird way.
There is an extremely disturbing episode, "Monstory", where Dee-Dee won't stop telling Dexter knock-knock jokes, and in desperation, he reaches into his jacket to retrieve a vial that will leave her mute. Instead, he obtains a vial that has a warning on it that drinking it will turn you into a monster. He gives it to Dee-Dee who turns into a horrific beast, and the episode essentially consists of the two of them going back and forth drinking the vial and increasing in size, but while Dee Dee gets more disturbing by the second, Dexter's mutations are weak to say the least, until he drinks the contents of a nuclear plant and grows into an enormous Godzilla like creature. The episode concludes with Dee-Dee becoming an ABSOLUTELY TERRIFYING spider creature that pins Dexter to the ground and speaks with a high pitched squealing, echoing voice: "So the boy told the girl in the park on the pony... 'Knock knock!'"
Not to mention that they get into an honest-to-goodness kaiju battle, and while it's more funny than scary (Dexter and Dee Dee even name the attacks they throw at each other), there's quite a bit of collateral damage to the city they're in.
The TRON parody episode, with the evil computer program's creepy, gravelly voice, how quickly it takes over the lab, and how Dee-Dee comes VERY close to not defeating him.
The episode "Star Check"—basically a Star Trek parody. Dexter and his friends want to go to a Trekkie convention, but end up in a Darbie (Barbie parody) collectors' convention instead. Said doll collectors look and act very much like Klingons. Especially when they accidentally open the box of a collector's item, which appears to be a capital sin around here. The expression on the other customers' faces is simply hair-raising.
The leader of the Darbie collectors, a hideous old crone whose prized possession is an original Darbie from the 50s still in its packaging.
The first season episode "Dee-Dee's Room." How does it begin? With a zombiefied looking Dexter with pulsating veins over his face. It ends that way too.
The crazy and unsettling music in the backround being played while Dee Dee and the rest of the family are making those disturbing noises doesn't help either.
Future Mandark's fate in "Ego Trip". His Fat Bastard body violently mutates, causing all his fat to shoot up into his cranium, making his whole body EXPLODE, leaving only his brain. It's one of the worst cases of Nausea Fuel in the show's history.
Dexter going insane and destroying his lab in "Way of the Dee-Dee". Not helped by the episode's Tear Jerker ending.
Dexter's Mom's mental breakdown in "Psylightly Psycho" can turn anyone into a germaphobe.
The dust bunnies. DEAR GOD. THE DUST BUNNIES.
In the crossover episode with Blue Falcon and Dynomutt, in the flashback, as Dynomutt confidently tells Blue Falcon where the stolen diamond's location was at, behind him, Buzzord stabs him through with his claws. Watching Dynomutt, the goofy sidekick of Blue Falcon, being stabbed by a ruthless villain such as Buzzord and seeing him cringing in pain. God, poor Dynomutt!
What happens when Dexter's parents don't have their morning coffee.
You could see that their dad was about to do something unspeakable to his own children, and the only reason they were saved was through a joke whose meaning (as a pop culture reference) is obscure to younger viewers. And even then, when everything is okay, the last line of the episode, "BUT WHAT IF WE DIDN'T.", takes it right back to terrifying.
Earlier in the episode we get a Gross-Up Close-Up of Mom and Dad's faces. It's... not pretty.
Dexter's parents and Dee Dee getting possessed in "Gooey Aliens That Control Your Mind".
"Ewww, That's Growth" has Dexter trying to accelerate his body growth so he can be big enough to ride a rollercoaster. His experiment succeeds, but as soon as they arrive at the rollercoaster, they must go down an impossibly long queue, and by the end, Dexter's gotten much bigger than most of the other people waiting for the rollercoaster. Once an elongated Dexter finally gets on the rollercoaster and enjoys the ride, his head crashes into the upper part of a tunnel. The scene abruptly cuts to a THE END card. And an uncomfortable feeling will most likely come over you.
Koosie's laugh in the "The Koose is on the Loose" can be pretty creepy, especially at the end when all it shows is the end card with no music and all you can hear is his laugh.
The episode's title card. While humorous, it's something you never thought you see the characters do in official artwork, especially in Dee Dee's case.
Dexter's guilt induced daydreams in "Space Case" including a giant fork like object heading directly towards Dee Dee's head, Dee Dee's arm being sliced in place of a sausage and Dee Dee's decapitated head on Dexter's plate!
Whenever Dexter's mom gets angry, she's pretty terrifying, especially in the episode "Dee Dee Locks And The Ness". It's no wonder why Dexter, Dee Dee, and their dad never say no to her favors.
"Dexter's Assistant", in which Dexter makes Dee Dee smarter. He does so by removing her brain, complete with opening up her head while she's still awake, taking out her tiny brain, and placing a larger, smarter one in its place!
The demise of the Energy Thief. Dexter turns an entire array of solar panels to converge their rays upon the crystalline beast, causing it to turn bright red and boil from the inside out before exploding into Ludicrous Gibs that splatter over everything. Gets a bit worse if you think about it too hard, as the creature was only taking energy from the solar plants to feed itself and continue living.
Most of the episode "The Bus Boy", revolving around kids stories about what lurks in the dark back of the schoolbus. Pleasant stories such as a giant monster that eats little children and appears as a giant fanged mouth in the darkness, a giant spider with a human head, and a tear in reality that drags in any child that strays too close. Worse, its apparently TRUE to some extent, as a boy named Billy had apparently disappeared back there decades earlier, and when Dexter drops his pencil near the dark area, something grabs it and drags it into the darkness. Thankfully, it turns out the "monster" is Billy himself, who got trapped in a wad of bubble gum and has been living back there ever since, but is quite a nice, well adjusted guy despite of this.