Mister Fantastic isn't necessarily the backbone of a team with his powers. Let's face it: he's basically the Elongated Man (at least Plastic Man turns himself into cool stuff like mailboxes and such). Fortunately for him, he's got bunches of brains to keep Sue attracted to him.
Though he's had his share of failures (the Thor clone), he's also saved the world a time or two from Galactus and various other cosmic villains Spider-Man wouldn't have been able to take down.
There must have been something special about him, because the Skrulls wouldn't invade until they knew he was taken down and captured. His people skills and common sense might need some work, but no one can knock his talents in creating gadgets.
He's not necessarily the smart one here, but he has the money and power to get what he wants. His scheming and manipulating ways make him a force to be reckoned with.
He's come very close in the past to taking down Superman, though he did meet his match when he tried to tackle Bruce Wayne (not realizing he was Batman). Still, Luthor has this ruthless greed that got him an Orange Lantern ring for a while, and still makes him someone every hero would be smart to steer clear of. He might not create toys like Reed Richards does, but he can sure turn a situation into his favor and devise some wicked schemes.
With all the different types of Iron Man armor he's come up with over the years, there's no way he could stay off this list. Even though he was responsible for the Marvel Civil War and the Skrull Invasion that followed, there's no denying he has technical smarts if nothing else.
He had problems with alcohol (and his "Ultimate" version still has some issues with it), but he seems to have rebounded nicely. At one time he was the head of SHIELD, and really started losing his way, but after Norman Osborn, the Skrulls, and the death and rebirth of Captain America/Steve Rogers, Stark seems to be leveling off again.
He's called the "Scientist Supreme" in the Marvel Universe. That means he's officially been crowned the smartest man in the Marvel U (though he's got perhaps the lamest title).
Pym has been responsible for a lot of big developments in the Marvel world. His most nefarious is Ultron, though in his defense he didn't create the robot to rule the world...he just did an incredible job of it.
Hank seems to perfectly illustrate what Marvel tries to convey about their characters: they are all only human. A man who constantly shrinks and grows has to have some side effects from that over time, and the constant pressure of being a hero, scientist, and husband has to wear on you. Pym has lost his way more times than any other hero on the list, but he always drifts back.
The one-time leader of the JSA is also a brilliant man in the DC world. He holds several doctorates and has come up with some pretty cool gadgets of his own.
I'm not a fan of this character's gimmick. This is one of those characters that is rebooted just to add diversity to the team. Rather than create a new character, they just named him "Mister Terrific" and made it seem like he was carrying on the previous version's work...except this guy is super smart and can't be seen by computers, whereas the original was just a fighter.
Still, you have to give him credit, he's created those T-Spheres that help him out a lot, and always seems to find a way to help the JSA out. When he and Doctor Midnight were forced by Roulette to play a "loser dies" game of chess, Terrific took the game to a stalemate and then got away before they could reset the board. Pretty smart!
He could be considered the evil version of Reed Richards, except Doom doesn't stop with science. He includes magic and whatever else it takes to help accomplish his goals.
While ruling the world has constantly evaded his grasp, his rule over Latveria has been fairly consistent. He's also created armor that's arguably comparable to Iron Man's. He also created a group of "Doombots" that take his place in most confrontations so there's seldom the opportunity to really take him down. He found a way to steal the Silver Surfer's power cosmic, and even almost outsmarted the Beyonder.
It's hard to think of a hero he hasn't faced. Everybody from Spider-Man to Power Pack can claim at least one run in with him. Still, he seems most closely linked to the Fantastic Four. Now that Norman Osborn's empire has been drastically reduced, it'll be interesting to see where Doom goes from here for revenge.