For the love of Bob Kane and Bill Finger, make another theard for DC characters.
To keep on topic;
1)Dr. Doom - I think during Waid's run, he commented that Doom was smarter than Reed, Doom’s Mad-On for Richards limits him. However, when he wasn’t focused on Richards and revenge, he’s done amazing things. He's taken over planets in canon with only having a few people who attempted to stop him but failed.
2)Mister Fantastic - Very intelligent, but has shown displays of a complete lack of common sense. It’s only been recently they’ve really pointed this lack of common sense out and that many of successes were also a stroke of luck. It was certain before Reed’s transformation, that Doom was smarter than him since the cosmic rays also heightened his intelligence.
3)High Evolutionary - From what little I read, he developed a way to lengthen his life span within a human lifetime. He might be over Richards and Doom, but considering that Doom and Richards have never made a bid to extend their life, this is questionable.
4)Tony Stark - It is certain that Tony is one of the three smartest man on the planet without additional abilities. Over all, he’s the 4th genius in the MU.
5)Mad Thinker - Written correctly, this guy can be a mad genius. He could top Stark if he focused on boarding his expertise, instead of criminal plots. If he wasn't a D-List villain, we could see more displays of his brilliance. He really does strike me as a Dr. Doom-lite.
6)Sinister - Considering his accomplishments before turned immortal by Poccy, Essex is smarter than Apocalypse. It was only after his transformation that allowed his genius to develop far beyond a normal lifespan.
7)Apocalypse - He's intelligent, but his wisdom comes from living for centuries and developing it. He’s cunning and has the largest capability of being a battle tactician and how to maintain a low profile, however.