Well... they have different fields of expertise. Personally my most brilliant would be Reed/Doc Doom. Just for easy reference (with my opinions.
Reed Richards - mechanical engineering, all levels of physics, Human and alien biology, chemistry. Pretty much a diverse field - totally forgot his biology expertise until I remembered a recent encounter between him and Spiderman discussing the Lizard. Still hasn't found a solution for Thing's condition. Doom and him are considered the experts on extraplanar/temporal travel.
Doctor Doom - Same as Reed but has certain fields that he probably has an edge on. Robotics (doombots over HERBIE any day...) and Sorcery (more like dabbles in magic - not Sorcerer Supreme level)
Phineas Horton - Creator of the (android) Human Torch I. "Advanced knowledge of Steel and Synthetics" (MARVELS) There was a WCAvengers issue where they explored the insides of Human Torch and found out that he built him from Vacuum Tubes and not the modern day transistor... amazing because that would make the Human Torch and Vision (identical to make as the Human Torch) the only robots that can withstand an EMP.
Tony Stark - Technological genius. Tony's strengths include skills from outside the scientist box. I think his corporate maneuvering knowledge, people and political skills give him the edge over the others as a pure power player. Also, I don't think anyone has built more machines on-the-fly than Stark has (tell me if I'm wrong - or hasn't Tony kit-bashed the most among all the heroes)
Hank Pym - chemist, biologist and roboticist. Pym probably has the edge on patents made over the rest. If Pym particles weren't enough to put him as the top genius in shrink/growth tech. I think he's also the 616's best robotics mind. Having created Ultron alone puts him in a class above the rest.
Bruce Banner - Nuclear Physics expert. I've never seen him do much in other fields.
Doc Ock - Robotics expert. But in Atomic Physics, He's as sought after as Banner in this field (he's usually a plot point somewhere if they need an expert consultation...) Madman drawback makes his intellect a waste...
Beast - Biochemistry and Genetics expert. Astonishing X-Men showed he wasn't the one that could invent a "cure" for mutation however. Cured the Legacy Virus, but not in time to save others affected by it.
Professor X - Genetics expert. I think he's the top expert in the field of psionics. He's the only one who teaches how to defend against psionic attack to non-psionics.
Dr. Moira Mctaggert - Another expert in genetic mutation.
Kitty Pryde - Computer expert. Though I've never seen it used much anytime I've read her. Can anyone cite examples? I have no gauge as to her ability.
Others off the top of my head:
Fixer
Mad Thinker
Puppet Master
Egghead
Paste Pot Pete/Trapster
Spiderman (inventing web fluid - or has this been retconned?)
Reed Richards - mechanical engineering, all levels of physics, Human and alien biology, chemistry. Pretty much a diverse field - totally forgot his biology expertise until I remembered a recent encounter between him and Spiderman discussing the Lizard. Still hasn't found a solution for Thing's condition. Doom and him are considered the experts on extraplanar/temporal travel.
Doctor Doom - Same as Reed but has certain fields that he probably has an edge on. Robotics (doombots over HERBIE any day...) and Sorcery (more like dabbles in magic - not Sorcerer Supreme level)
Phineas Horton - Creator of the (android) Human Torch I. "Advanced knowledge of Steel and Synthetics" (MARVELS) There was a WCAvengers issue where they explored the insides of Human Torch and found out that he built him from Vacuum Tubes and not the modern day transistor... amazing because that would make the Human Torch and Vision (identical to make as the Human Torch) the only robots that can withstand an EMP.
Tony Stark - Technological genius. Tony's strengths include skills from outside the scientist box. I think his corporate maneuvering knowledge, people and political skills give him the edge over the others as a pure power player. Also, I don't think anyone has built more machines on-the-fly than Stark has (tell me if I'm wrong - or hasn't Tony kit-bashed the most among all the heroes)
Hank Pym - chemist, biologist and roboticist. Pym probably has the edge on patents made over the rest. If Pym particles weren't enough to put him as the top genius in shrink/growth tech. I think he's also the 616's best robotics mind. Having created Ultron alone puts him in a class above the rest.
Bruce Banner - Nuclear Physics expert. I've never seen him do much in other fields.
Doc Ock - Robotics expert. But in Atomic Physics, He's as sought after as Banner in this field (he's usually a plot point somewhere if they need an expert consultation...) Madman drawback makes his intellect a waste...
Beast - Biochemistry and Genetics expert. Astonishing X-Men showed he wasn't the one that could invent a "cure" for mutation however. Cured the Legacy Virus, but not in time to save others affected by it.
Professor X - Genetics expert. I think he's the top expert in the field of psionics. He's the only one who teaches how to defend against psionic attack to non-psionics.
Dr. Moira Mctaggert - Another expert in genetic mutation.
Kitty Pryde - Computer expert. Though I've never seen it used much anytime I've read her. Can anyone cite examples? I have no gauge as to her ability.
Others off the top of my head:
Fixer
Mad Thinker
Puppet Master
Egghead
Paste Pot Pete/Trapster
Spiderman (inventing web fluid - or has this been retconned?)