I think he means Batman with Ray Palmer in his ear is the top super-genius. I’ll stick with Mister Fantastic, though; he’s the only one listed thus far whose managed to maintain a loving monogamous relationship.
Let me try a diffrent tack.
“Evil always wins, because good is dumb” DarkHelmit
Which one here is the most Nasty? Judged baised both on appearence and on actions, by Dark Helmet.
Brainiac Five
Did some thing or another, and looks like either Spike, or a green guy, depending one which version you see. Yawn His action figue is really boring.
Mr. Fantastic
Likes to play tentacle moster with Ms. Fantastic when he thinks they are alone. Wrong kind of nasty. Let’s move on.
Lex Luthor
Has a purple and green battlesuit. Hasn’t actually done much, accept to try and kill people, all of whom are saved by Supes.
Penny
Not evil, but she has a kick ass theme song.
Angus MacGyver
If it was just him and Batman, he would win. But it isn’t. Besides, themullet actually suits him, and he isn’t evil. (Enough)
Victor Von Doom
Actually quite evil, but stuid enough to cover up a perfectly good face with a red-hot mask, scarring him for life. So stupid he may as well be a good guy.
Batman
May or may not have killed a few thugs, werewolfs and vampires. Dresses Evil. A definite maybe.
Mr. Mind.
Just look at the little Green Bugger. Nasty looking and smug. Just like me. Has the highest body count I have ever seen.
I forgot to mention Ray Palmer, who isn’t evil, and doesn’t get the idea that the proper thing to do when inside someone’s ear is to controll their mind, not give advice, or-
Ewwwww.
I’m tied between Mr. Fantastic and Brainiac 5. Brainiac is smarter, but Mr. Fantastic seems mentally and emotionally healthier. That’s also part of why I discount both Doom and Luthor; besides the fact that they tend to ultimately lose, neither is very well wrapped.
If the crazed/obsessive part doesn’t bother you, I’d also like to mention Thanos and The High Evolutionary as mad geniuses.
Ooh,
I nominate Metron of the New Gods.
Pros: Master of Clarkeware. Blurs the line between technology and magic, alien and god. Invented the Boom Tube and the Moebius Chair, which totally makes time and space his bitch.
Cons: Vaguely immoral. Often does the “disinterested observer” thing. Will totally sell you out to Darkseid for a snort of X-Element. Gets out of his chair less often than Professor X.
Looks like a tool in that costume.
Nah, Doom has conqured the known multi-verse twice. Braniac never even gets close. The only thing that can defeat Doom is Doom. He hates himself so much that he usually causes his own demise. Doom with Richards a close second. He’s another walking plot device.
Well, I think they’re comparing Doom to Brainiac Five, not the super-villain. If you take points from Legion-of-Super-Heroes Brainy for not conquering the universe (which he isn’t trying to do), you have to take points away from Victor V. for curing Mon-El’s lead allergy. 
Barry Ween smokes the lot in about six seconds. Best friend Jeremy asks when did MacGyver ever have a comic book, anyway? Barry slaps forehead in frustration.
I meant to change the subject line to merely “super-geniuses,” but clearly I forgot.
Syndrome
Pros: Smart, motivated, and a quick study: went from annoying brat to genius multi-billionaire in 20 years, without benefit of superpowers, pacts with dark forces, or loss of limbs and/or facial mutilation.
Capable of beating any given super with an array of self-invented weapons of awesome destructive might, yet smart enough to delegate: employs competent, ruthless henchmen who shoot first and don’t balk at killing women and children.
Has the sense to test his destructive devices first, thus refining them while quietly taking out most of the potential opposition.
Really cool island lair. Probably hopping on with Mirage. Still has own hair.
Cons: Still annoying, and thinks too small. Wishes to impress rather than conquer: motivation is desire for acclaim rather than lust for power. Too needy, really.
Relative inexperience causes fatal cockiness: tendency to strut and posture, and doesn’t test destructive devices enough. Should have watched Robocop before completing final Omnidroid. Over-confidence leads to trusting sexy assistant, whom he doesn’t watch closely enough.
Cape. Still has own hair.
Verdict: A very promising start from a gifted beginner, but sadly let down by over-confidence and lack of experience. Ruthlessness fatally compromised by pettiness and lack of ambition. In a continuing series, would have survived the fight with the jet intake hideously disfigured but wiser and hellbent on vengeance. Hope for a sequel.
Ok, if we’re not limited to comic books then here’s my nominee:
Wile E. Coyote
Pro: Unlimited credit line with Acme. Comes up with incredibly complex devices, often made from unassuming household items. The only one of the lot to have actual business cards labelled “Super Genius.” Still has his own hair.
Con: Has never actually caught the Road Runner (well, maybe once, but was that canon?). Plans always backfire, frequently because of his own distraction. Has yet to figure out that Acme Catering Services can probably whip up southern fried road runner and deliver it right to his cave. Lives in a cave.
Verdict: Wile E. will never win, but a clever strategist could maneuver his enemies into allying with Wile E., with the guaranteed result that Wile E. would inadvertently take out himself and his allies in as spectacularly embarassing a way as possible.
Of course, Syndrome’s the only other one here enough of a dumbass to fall for it…
So…Syndrome and Wile E. taken out in the first round, everyone else laughing their brilliant rear ends off.
So it looks like Destro is winning, because whether Cobra wins or loses, he still makes money, & has his own outfit.
When Cobra Commander had to go into hiding, Destro just lounged in his castle in Trans-Carpathia.
Nuts. I was just about to mention him.
Professor Ivo. Why? Because he built a sentient robot that could duplicate anyone’s powers. Anyone. Why bother to conquer the world, when you can send your lackey to do it for you?
Also, someone must name Anarky, as a relative newcomer with real potential.
Nobody’s mentioned Professor X or J’onn J’onnz?
We must add to Braniac’s pro’s the fact that his banjo-playing abilities are lauded in a well-known Spike Jones melody. This alone puts him over the top in my book.
Ya know, given that the X-Men have the highest casualty rate of any super team in comics (except Strikeforce: Morituri, of course), I’ve always been suspicious of his genius status. As well as his leadership abilities.
J’onn seems to be biology/medicine oriented.
What about Stormwatch?