Clever or Intelligent Main/Supporting

[ReAcrylicMetal]

As the title states, I'm looking for some good anime or manga with intelligent or clever main or important characters. Preferably ones with non romance driven plots.

Ones I've liked so far:
Mushi-shi*
Full Metal Alchemist
Level E*
Code Geass
Darker Than Black
Utawarerumono*
Spice and Wolf*
Bakemonogatari-has romance but was still very enjoyable
House of the Five Leaves*
Spiral (only seen an episode or two but seems pretty good so far)

Manga:
Gamble Fish*
Iris Zero*
Zippy Ziggy
Dorohedoro

Things I disliked or got tired of:
Bleach(and others with similar mains): Although I loved many characters of the above description in Bleach, Ichigo's never changing strategy of charging in without thinking ultimately made me drop the series. (Orihime's uselessness didn't help)
Honey and Clover: Again, loved many of the characters and the art student plot, but the romance part between Hagu and Takemoto resulted in me dropping it. (At least for the time being)

Anime List
(Haven't made a list of manga yet...)
Feel free to recommend anything on the dropped, on-hold, or plan to watch lists, as I probably won't get to them for awhile unless I'm given reason to watch them.

[Sackett]

Crest of the Stars - I think this would be perfect for you. Great characters, great plot.

MxO (manga) Boy with no magic ability sneaks into a magic highschool. Now he must convince everyone he has magical powers, even though he doesn't. Mainly he uses a combination of intelligence, trickery, and sheer guts.

The World God Only Knows Okay, so yes this has romance... sort of. Basically Keima, the lead character, is an expert dating sim gamer. He receives a challenge asking if he can capture any girl. Assuming this refers to game girls, he accepts- oops. He just made a deal with the devil that will cost him his head if he can't make real life girls fall in love with him.

Since real girls detest the real Keima (ie he's a four-eyed geek), he has to come up with a web of lies, deceit, and manipulation to get the girl to fall for him. Then he has to move on to the next girl. The plot grows more and more complicated in the manga, as Keima tries to figure out how to get out of this mess. The anime seems to be a pretty faithful adaption, but the first season never got beyond the early arcs, which don't have as much of the interesting twists and turns. (Second season is due out this spring)

The Melancholy of Haruhi Suzumiya (although granted this is more so in the novels- apparently Kyon must use scientific journals as light reading considering all the little bits of science trivia he drops during his internal monologues).

Baka to Test. Okay, yes, so most of the cast are idiots- Okay, actually all of the cast are idiots, but that doesn't stop the leader of class F from actually being extremely clever (he used to be a child prodigy you know). Personally I prefer the manga/novel plot line to the anime, but they are both decent.

Have you seen FMA: Brotherhood? It's worth watching if you've only seen the first anime.

[ReAcrylicMetal]

Thanks
Crest of the Stars- Sounds good, I'll go watch a bit of it now
MxO-Sounds especially interesting, will probably get to some of it tonight as well
The World God Only Knows+The Melancholy of Haruhi Suzumiya- I've been meaning to see these for awhile. They seemed more light hearted when I first glanced at them, but I'll be sure to check them out now
Baka to test-xD Sounds amusing
Brotherhood-Yup. Seen it, love it.

Any more suggestions are much appreciated

[GreatTeacherKen]

Jojo's Bizarre Adventure- a long running action manga with different story arcs that focus on a different set of heroes. It's not absolutely necessary to read the story arcs in order, but reading them in order does make a few plot details clearer.

All of the protagonists are highly intelligent and most of the fights are won with clever tactics and applications of their powers. Even powers that sound completely useless often become deadly with the right application. This is especially evident once the Stands are introduced in Part 3 (Stardust Crusaders) and is also when the fights get really crazy.

It should also be noted that the villains are for the most part not idiots either so the fights aren't always easy for the heroes and quite a few of them don't make it to the end of the story arc.

In terms of intelligence, Joseph Joestar, the protagonist of the 2nd story arc, sticks out since he uses a lot of dirty tricks in his fights and although he's not omniscient he is able to predict what his opponents to say next.

[Guardian Enzo]

Seirei no Moribito is filled with smart folks generally, but the male lead is especially smart and has a couple of eps dedicated to his mental prowess. The joy of the series, though, is that almost all the major characters are smart people dealing with difficult situations.

[Konakaga]

While most of the characters of Needless aren't too smart or witty, Cruz is pretty clever in use his observations to figure out the secret or trick that their opponents use in their skills. [note won't show right away]

Togame, self titled "stragian", of Katanagatari, is very clever she since creates the tactics to either earn the swords or to defeat their owners. And generally prefers attempted negotiation before fighting .

Also I'll give Seirei no Moribito, The World God Only Knows, and The Melancholy of Haruhi Suzumiya a seconding.

[Ziziphus]

For anime:

- Monster has one of the most brilliant antagonists you've ever seen in anime. The main lead is also very clever. A brilliant anime overall. Highly recommended!

- Umineko: the main character tries to win a battle of wits against a witch, over and over again. The anime never reaches the true conclusion of the novel, but what it has to offer is enjoyable enough for me.

For manga:

- Liar Game and One Outs. From the same author, both have uber clever protagonists and exciting battles of wits.

- Houshin Engi (or Soul Hunter): the main character, Tai Kou Bou, is based on a famous strategist from the Yin Dynasty of ancient China, albeit a more mischievous version. The manga is finished and highly recommended. I don't recommend the anime adaptation though.

- You can also check out the never-ending Detective Conan (or Case Closed) for the high school genius detective Shinichi Kudo.

[kona~chan]

try Akagi and kaiji both comes from same author and already adapted to anime, the story mainly about gambling, but akagi more focused in richii (japanese mahjong) so maybe little hard to understand if you don't know anything about richii.

[Niji]

Guin Saga has an intelligent main, and some important chars. Also, I see you rated Utawarerumono pretty high, it is somewhat comparable in topic.
Black Lagoon also has an intelligent main. One has to have a high tolerance for gore and violence though, and specially 2nd barrage is quite gruesome at times.
In case it can be SiFi and old, Legend of Galactic Heroes has several very intelligent characters.

[mecharobot]

Master Keaton. He is the anime MacGyver.

[Tri-ring]

I second Master Keaton An archeologist, a former SAS survival instructor, an insurance op and foremost a humanist.

I also recommend Gallery Fake. Fjita Reiji, an enigma with vast knowledge and passion in fine arts.

[SeijiSensei]

Wow, you're sixteen, and you liked House of Five Leaves? You're on the road to being a woman of great taste.

I was about to recommend Mononoke, but you've seen it already! In that case I recommend the original version of "Bakeneko" which comprises the final arc of Ayakashi Samurai Horror Tales. It's very different from the version of "Bakeneko" in Mononoke, and to my mind, a better one.

Another possibility might be Nijuu Mensou no Musume, a story about a master thief who rescues a young heiress from her predatory step-parents. Both the thief and the heiress are very intelligent.

You also might enjoy Mouryou no Hako. The most intelligent character, Kyougokudou, doesn't really appear until midway through the story, but there are some other bright people in the show as well.

The heroine of Saiunkoku Monogatari is a very smart young woman about the same age as you. She seeks to become her country's first Imperial official. There's romance in this story, but Shurrei never lets it distract her from her goals.

Another smart young lady is the heroine of Kemono no Sou-ja Erin, based on a novel by the author of Moribito.

There have been other excellent suggestions, but I particularly want to endorse Monster. You can watch it online legally at Hulu.

Let me add three other shows that are "smart" overall, though the protagonists aren't themselves all that intellectual. One is Ghost Hound, about a middle-school boy who's being treated for post-traumatic stress disorder arising from being kidnapped at age four.

Then there's Oh! Edo Rocket, where a young fireworks maker in 1843 Edo (Tokyo) is approached by a mysterious woman who asks him to make her a rocket that can reach the moon.

Finally I'll suggest Baccano! Some of the characters, like Maiza, Chez, and Nice, are quite smart; some, like Issac and Miria, are incredibly dumb; and the rest are somewhere in between.

All three of those links point to legal streams.