One episode started off with Dexter and Deedee flushing their dead fish down the toilet, later the ghost of said fish comes back to haunt them. The ending parodied the classic ending from Michael Jackson's Thriller.
The episode "Jeepers Creepers Where Is Peepers?" featured Dexter and Deedee's magical friend Koosie working together to save Peepers (another magical being), in one scene we see a rather disturbing graphic look at Peepers as he is having his energy sucked off.
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.
There's the Chicken Scratch one too. And the Bus one. Although the guy lurking at the back of bus which was quite a nice, jolly big guy.
There is an extremely disturbing episode 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. 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.
The Tron parody episode where the evil deep-voiced computer program takes over the lab and Dexter and how close Dexter and Dee-Dee come to not defeating him.