Smart Shounen Protagonists

Every shounen anime/manga has a complete and total moron for the main character right? WRONG!  Yes, some of the most popular ones are incorrigibly unintelligent, (I'm talking about you Luffy) but these main characters are possibly the smartest or most knowledgeable character in their show.  Or at least, the smartest guy in every room they enter.  I did not add any female characters to the list because I felt the stereotype only applied to male characters.

Toriko (Toriko) -  Toriko is extremely knowledgeable on topics concerning food and their ingredients.  On top of this, he has a large amount of biological and behavioral knowledge about many of the countless animals on the planet.  He is also well versed in methods of capturing and killing these animals. 

Yoshino Takigawa (Blast of Tempest/Zetsuen no Tempest) 
Yoshino is cold and practically heartless.  Of course, like most cold heartless anime characters, he is extremely intelligent as well.  He outwitted the evil mastermind of the series in an intense, stressful situation where the fate of the planet literally hung in the balance.  He did this without even having an ample amount of working knowledge on the subject matter. 

Lelouch vi Britannia (Code Geass: Lelouch of the Rebellion)
This high school student is a master of chess.  Most if not all of us know that chess is a highly strategic board game where the person with the higher intellect is more than likely going to win.  He easily wins matches where he is given handicaps that are impossible to overcome.  He also outsmarts high ranking military leaders on the battlefield and treats as nothing more than an extremely easy game of chess.

Shiba Tatsuya (The Irregular at Magic High School/Mahouka Koukou no Rettousei)
In a world where magic exists through technology and each spell is akin to a computer program, Shiba Tatsuya is able to not only create new spells, but read the various sequences others put into casting them.  Because of the nature of magic, this can be seen as reading the entire coding for Notepad in the blink of an eye.  On top of this, he invented a way to negate the magic sequences of others with extreme efficacy.

Shiroe (Log Horizon) 
As far as can be told from the 25 episodes of Log Horizon, Shiroe is by far the best strategist in the anime.  He quickly formulated multiple plans that worked without a single flaw and even outsmarted all the plans of others.  Often doing so with relative ease.  He was even able to comprehend the new physical laws of the game and figure out how to create a new magic that would rewrite one of those laws on a moment's notice.  He is also capable of predicting the next 30 seconds in a battle with only a 1% error margin through sheer intellect.

 

Light Yagami (Death Note)

 

Light Yagami is a student that got the 100% of questions on the college entrance exam correct.  He is also able to have a battle of wits with someone who is arguably the world's greatest detective and read through several of his plans to expose Kira.  Light Yagami has outstanding skills of deduction as shown when he was able to deduce with amazing speed that not only was his bedroom entered, but it was likely bugged as well.  He shows these skills again when he is able to figure out whether or not he should win a game a tennis to keep his identity as Kira a secret.