The Adventures of Jimmy Neutron: Boy Genius/WMG

The reason Jimmy's father acts rather dim is almost certainly because he caused himself brain damage by smoking weed.
Let's start with the question of how a boy as smart as Jimmy could have a dad as dumb as Hugh. It's genetically impossible, right? Well, maybe it would be impossible if you believed that Lamarck Was Right. But we know that Hugh could have an acquired condition that made him dumb, but still had smart genes to pass on to Jimmy.

Still not convinced? Well, I refer you to the episode where Jimmy time-travels back to the time when his father proposed to his mother in the seventies. Jimmy's mom called him by the nickname "Hughby-Dooby." 'Nuff said.

And this may not be relevant, but notice that there's only one letter of difference between "Hugh" and "High."
 * Most subtle Drugs Are Bad message ever. This also explains his obsession with ducks to the point of Cloudcuckoolander.
 * It's hardly "genetically impossible." Unlikely, yes, but human intelligence-- inasmuch as we even have a semi-clear definition of just what that quality is-- is determined by a myriad of interacting genetic and environmental factors. Plenty of room for a high IQ to skip a generation.
 * Also it was implied on the episode "Clash of the Cousins" that the Neutrons have "dominant genes" for stupidity and obsessiveness and Stupidity (Hugh was fortunate enough to get both his love for ducks and low IQ respectively. Jimmy and Eddie inherited the rare Neutron "genius gene".

Beautiful Gorgeous writes ZADR fan fics in her off-time.
"You're so brave and cute for such a green guy." After that one line, she grew an infatuation with him and It Got Worse.

Jimmy's Mom is just as intelligent as he is
She even studied at college but gave it up for - guess who - Hugh. And pie-baking. She has often shown sudden outbursts of scientific knowledge, that even rival Jimmy's.
 * Since the show is set in a city that seems to have stopped at the 50's, it'd make sense. Mainly because she'd be poorly-viewed by others if she opted for a career instead of being a housewife.
 * So that's where Jimmy got his intelligence from. Maybe Jimmy's Mom's side of the family are all intelligent.

The "dumbing down"-helmet left Jimmy unable to stave off Hollywood Science and Aesop Amnesia
Alternatively, it has an area effect, leaving everybody unable to Think Of The Potential if they'd just repair the flaws of the Black Box.

Jimmy killed the blimp pilot in the election episode.
The three candidates were disqualified due to being guilty of blackmail, fraud, and murder- no, wait, operating a blimp on school grounds. Mrs. Fowl didn't want to cause a panick, and Jimmy used his hypno-ray to erase the information from any witnesses' minds. Alternately, goat-kebab boy was guilty of murder, and Mrs. Fowl disqualified Jimmy instead so as not to incure his wrath.

The Nobel Prize judge was part of the Free Energy Suppression Conspiracy.

 * See the Wall Banger/Western Animation section of Wall Banger for details.

Sheen is an experiment gone wrong by Jimmy.
In one episode, Sheen pretended to be the genius in order to impress someone, and says that Jimmy was a failed experiment. Could the reverse be true? (Also, I don't recall ever seeing his parents.)
 * Actually, you do get to see Sheen's dad: Both in the end of The Movie ("Ultra-Dad!" "Ultra-Son!") and in the made-for-tv movie where the kids have to compete in an intergalatic reality show; he's in the group of parents that's rigging the portal on Earth to try and get the kids back home.
 * And also a couple other episodes. He apparently works as some sort of mechanic.
 * Air-conditioner repairman.
 * Sheen's dad is even the focus of one episode and briefly becomes a superhero to impress Sheen.

Jimmy is a Genius.
Carl and Sheen are his Beholden, and the reason everything he invents goes awry/berserk is because of Havoc. The reason he doesn't display typical Genius behavior is that he's unaware of other Genii in the world.

Jimmy will grow up to become a spy in the future
The episodes featuring Jet Fusion and Professor Calamitus are clues.

Jimmy will grow up to bring The End of the World as We Know It, a Dystopia, or will just stop inventing altogether
Almost every episodes are a clue. Jimmy's inventions bring much more chaos than the satisfaction of the people. His inventions seem much more immoral to the masses. So Jimmy's fate has two choices: either to stop inventing and do not contribute to the progress of the world, or, he would just keep on inventing and bring chaos and destruction.
 * The episode where Libby becomes a dictator in the future is a clue. The original timeline where Jimmy keeps on inventing is not actually a utopia: it is a Crap Saccharine World where Jimmy rules a scientific dictatorship. In the timeline where Jimmy stops being a genius, his nonexistence causes a power vaccum where a Cleopatra-lookalike named Libby takes over.
 * That sounds like the "Ultimate Enemy" episodes in Danny Phantom.
 * Jimmy grows up to become Flint Lockwood.

Hilgo from "Time is Money" is Cindy in that future.
Being so rich, Judy and Hugh Neutron bought Retroville, leaving everyone else in the town extremely poor. Cindy grew depressed and slowly became.... that, and forgot how to speak. Except for the simple grunt "Da!". Hugh, to humor her, gave her a job as Jimmy's ugly, maid, nanny, THING.

Jimmy Neutron has a itty-bitty bit of Klingon in him.
Due to his large head, all he is missing is the ridges, dark skin, scary teeth, and the other Klingon traits. Sadly, his heart is not Klingon, for he thinks like a Vulcan.

Mc Spanky's is an actual burger, like one that would be eaten by a real-world human
Nicktoons Unite! has him interact with SpongeBob. The Movie shows SpongeBob to be very small. So there.
 * This extends to the Lollipop on top of the Candy Bar, and any and all other giant inanimate objects in the series as well.

Jimmy Neutron will grow up to be Howard Wolowitz.
Why not?
 * Alternatively, Sheen Estevez becomes Howard Wolowitz. His enjoyment of catfights certainly lends credit to the idea.

Cindy is a child of Athena
If we're going by the Percy Jackson continuity, Cindy fits the description of an Athenian to a T. Not to mention she does Tai Chi, a form of martial arts used for battle, she's highly intelligent, exhibits hubris, has many talents in building things, and we never get to see how she spends her summers. The only reason her grades are lower than Jimmy's is because of the ADHD and dyslexia that demigods naturally have.

The Complete Monster planet wasn't actually destroyed.
It just looked like it did, instead, it was teleported into an alternate universe where everyone is a doll. The inhabitants began making evil versions of every other living person. Jimmy was forced to have a doctor he knew monitor them, and make sure they didn't try anything funny. Unfortunately, the doc went mad, and soon he grabbed a chicken from the side of the road to watch the folks because he didn't care anymore.