Mandark is either a Magnificent Bastard or completely unnecessary to the show.
Big Lipped Alligator Moment: The part of "Continuum of Cartoon Fools" where Dexter holds a stopwatch while periodically saying 'BAAAAWT'.
Actually if you ever did timing scripts for animation dialogue you know exactly what he's doing, Word of God says that he was timing a storyboard of the cartoon itself, yet indeed, there was no other reason to put it besides it was funny.
"Computer, make me a sandwich!"
The ending of "That Crazy Robot!" where Dexter shoots lasers from his eyes.
Broken Base: Over the 3rd and 4th seasons. Some fans think they're completely terrible, others agree but consider a few episodes to be pretty good.
Cargo Ship: Dexter really loves his computer. And the feeling's mutual.
Fridge Logic: In "Photo Finish" when Dexter infiltrates a photo processing place to retrieve photos of his lab and comes across the alphabetical storage room, he checks every single section rather than just the one corresponding with his last name (whatever that is).
Genius Bonus: A lot of gags on the show are science references, some of which are fairly obscure.
Idiot Plot: The episode "Sis-Tem Error" has Dee Dee accidentally shutting off the lab's power and spending the rest of the episode tricking Dexter into thinking nothing is wrong by disguising herself badly as Computer, Robot and Mandark.
Seasonal Rot: The two seasons made without Genndy Tartakovsky after the show was Un Cancelled due to boring plots, ungodly amounts of Flanderization, and a really unfitting art style. Plus, they got rid of the Justice Friends and Dial M for Monkey segments.
Self Fanservice: Dexter and Mandark get a lot of this in fan-art.
Tear Jerker: The wacky and fun episode of Dexter having to deal with Deedee's imaginary friend hanging out with him ends with Dexter wishing away the imaginary friend, and commanding him to never come back again. And he does. Deedee runs away sobbing. Then it fades to credits.