My opinion is that the smartest villains are Lex Luthor and Ozymandias
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The Riddler! 
Lex, Slade Wilson and Ozy.
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You’ve got the same thread up twice just so u know. Beyond that, it depends on what area of intelligence you’re inquiring about. If u google it will say Lex Luthor, T.O. morrow etc. but most people are gonna say whoever they like the most or are most familiar with.
Sorry, my power went out while I was posting. To finish, I’d say Luthor overall, T.O. Morrow for robotics & Mr.Mind for schemes/ traps. Good question tho, Idk if the can be an absolute correct answer but I like reading everyone’s opinions.
The=there
The Joker 
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Vandal Savage, has thousands of years of knowledge
Brainiac, I mean he literally has “Brain” in his name.