These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
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.
Crowning Moment of Funny: "ARE YOU CRAZY?! YOU JUST THREW A DUCK AT ME!!" note The latter is said by Mandark's dad in the episode My Dad vs. Your Dad when Dexter's dad does, you guessed it, throws a live duck at him. An epic duck fight ensues.
Draco in Leather Pants: Mandark gets this treatment a lot. It helps he's more of an ass than an actual villain.
Dude, Not Funny!: Dexter's parents making him sleep in a doghouse at the end of "The ol' Switcharooms" because he totaled Dee Dee's room (not that she never had it coming) is more inhumane than funny.
A lot of people also hated the end of "Dexter vs Santa's claws", just to elaborate Dexter almost ends up killing Santa Claus and shaving off his beard just because he believed Santa to be his father.
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.
Val Hallen is blonde, based on a Swedish god, dumb, wears black, and plays lead guitar. Skwisgaar Skwigelf from Metalocalypse is blonde, Swedish, can't find his biological father (leading him to believe he's part god), dumb, wears black, and plays lead guitar. Cue WMG that Val Hallen's his father.
In the Mexican dub of the pilot episode, when Dexter is turned into a rabbit, he adds the line"What's up, doc?" Years later, Dexter first actor from the dub becomes the current voice of Bugs Bunny.
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.
Rewatch Bonus: Ego Trip features a clever little detail that hints at the ending. The robots that come back to the present don't attack Dexter or try to fight him even as he destroys them. The first time through, it just seems like Dexter was too fast for them. The second time you realize it's because Dexter built them and they weren't there to attack him in the first place. Dexter's egotistical belief that he had to be the one who saved the future started the whole plot.
They Wasted a Perfectly Good Plot: Some fans think the Uncancelled episodes had some genuinely neat ideas (like a backstory for Mandark, more focus episodes for Dexter's parents, the return of "Go, Dexter's Family Go!", etc.) that were bogged down by lackluster writing and animation.