To make it short, this is my list in order:
*Not including Kaito series characters
1. Akai/Okiya, Furuya/Amuro, Kudo Yusaku, Heizo Hattori, Gin, ANO KATA, Shukichi Haneda, RUM
All of them tie, here is my reasoning:
Ano Kata - Deserve to be regard as "the most smartest and have a smart strategy thinker" and all, the BO have been going on for more than 50 years at least and remain uncaptured by everyone. One must be damn smart to be in this posotions, not to mention, CIA, FBI, JSP have infiltrate the BO for everyone know how long and yet FAIL to bring down the Organization, nuff said.
Akai Shuichi/Okiya Subaru - He is smarter and above Conan/Shinichi IMO. One argue that it was Conan who plan his faked death BUT, we must consider that the reason Conan can come out and think of such plan is because he is aware about 2 things:
1. Professor Agasa Gadget to use as disguised
2. Kudo Yukiko, he know his mom is master in disguised and can help alot.
Conan are aware of that, while Akai don't. If Akai know of such Gadgets, disguised technique and all, he might as well come out and be able to think of such plan, even greater. As Okiya, he seems to solve the case faster than Conan, for example, the Kudo Yusaku's Cold Case, heck he even gave a hint to help Shinichi solve the case.
Furuya Rei/Amuro Tooru - Well, no need any explaination, he saw through and discover that Akai/Conan/Kir faked Akai's death by his own. Conan even need a help from Yusaku to confront him in Scarlet series, technically its 1 vs 3 (Akai, Conan, Yusaku) and guess what? He succeed and find out what he need to find - Akai is alive.
Kudo Yusaku/Heizo Hattori - They seem to be smarter than their son and a step ahead, though they lack a feat because of less appearence, but they are obviously among the smartest character.
GIN - This bastard is damn smart, he manage to beat Conan in all their encounter or shall i call it as "straight fight" ?? For example, the Itakura case, heck he seems rather supposedly stop at the last locker Conan in, but of course, thats just an assumption till now. The FBI fail to catch him, he is a smart leader in his own as shown as he give order to order agent even Vermouth about the plan and such, The Boss seems to trust him enough to handle alot of case, that must mean that he is damn smart because The Boss is also smart. They are also seems oftenly "talk" and discuss things along each other. What keep Conan save from him is just 2 thing:
1. APTX4869 - Anyone, i mean ANYONE even Kudo Shinihi himself would find it absurd that an adult can shrink and turn to be 7 years old, of course Conan accept and find it "logical" because he experienced it himself - the shrink effect.
2. Vermouth - For whatever the hell the reason
Shukichi Haneda - Lack of feat, however, he was shown to be smarter than Conan, no much can be said about him, let he appear more and show his true brain power.
RUM - Same, lack a feat too like Shukichi to put him in 1st Tier of smartest characters, but for the sake of HYPE, lets assume so. The fact that no one know "his" identity, even the BO itself must mean he is a greater threat, even greater than GIN himself. The only one who we can assume to know RUM identity is probably Ano Kata and thats it.
2. Kudo Shinichi/Conan, Heiji Hattori, Miyano Shiho, Vermouth
Kudo/Heiji - they seems to be equal at this rate, but of course people are leaning towards Conan because he is a main characters and have much more appearence, in other words much more feat for him.
Miyano Shiho - She is the reason this series is going on until now, nuff said.
Vermouth - Conan would die if not for her whatever the hell reason for not telling the drug effect to the BO. But she also seems to have an advantage beforehand that might not be count to her intelligence, that is she is aware that DEAGE is possible, she herself did not age for whatever reason, so unlike other Characters who find it impossible, absurd, and illogical, Vermouth awareness of this matter make up for her lack of "brain raw-power" compare to, say, GIN, Bourbon/Furuya, Heizo and etc
Theres alot to explain, but as for the rest, here is in my opinion about the rank(there might be some error though) :
1) Akai/Okiya, Furuya/Amuro, Kudo Yusaku, Heizo Hattori, GIN, ANO KATA, RUM, Shuukichi Haneda
2) Kudo Shinichi/Conan/Heiji
3) Miyano Shiho/Vermouth
4) Sera Masumi, Professor Agasa, Kir, Jodie Starling, James Black, Kansuke Yamato, Koumei
5) Mouri Kogoro, Eri Kisaki, Kudo Yukiko
This is it in my opinion about the smartest Characters in the series, well, doing list like this might be confusing and subjective though........ I might left out many other characters in the list considering there are too many character at this rate, so mind to point it out to me.
And for some characters, i put them in the same tiers to avoid any further freaking long explaination and confusion LOL!!
Make your own list.