My answere depends on what kind of smart we're talking about here. There's the kind of smart that is better suited for combat, by that i mean analytic abilities, deduction skills, and overall comprehension of a situation. Based on that i would make my list like this
1-Shikamaru(with an IQ of 200+ he has also displayed his intelligence, strategic planning, and overall intelligence in combat.)
2-Itachi(so many fan boys have made the statements so i don't need to say anything...)
3-Kakashi(kakashi is both very overrated and underrated but one thing people can't deny is his intelligence and intuitive aptitude)
4-Kabuto(his kind of intelligence is book smarts but he is very clever, manipulative and deceitful.)
5-Jiraya(he's the kind of guy that lacks the book smarts but makes up for it with combat wits, analytic skills, and overall thinking under pressure)
6-Naruto(Hate to say it but his intuitive skills, comprehension, are completely changed)
7-Sasuke pre shippudden(i did this because he doesn't really put much thought into his moves as he used to, in one word...Arrogance.)
8-Minato(i put him him here because we only saw him in one fight...He did well but it wasn't to hard figuring out that Tobi/Obito was using the same technique as him, almost no other character understood what he was doing so kudos. But still he was using the same tech so it was easier for him to comprehend.)
9-Darui(his stronger skill in the intelligence department would be his awareness of his chakra levels and the sufficiency with the tools and the chakra. He has and the way he adapts to different situations he is clever swift in adapting.)