Rowen Hashiba is described by Dais to be the smartest and most cunning of the Ronin Warriors. He probably got his smarts from his Mad Scientist father and is said to have a really high IQ.
Seto Kaiba of Yu-Gi-Oh!. Built up the world's biggest gaming company, designed three different card playing machines with excellent holograms, designed a card playing field on top of a blimp, and has computers that can do just about anything with the right operator at the keys.
There are plenty of cases of smart women among the twelve HiMEs of Mai-HiME, but the standout is the Shrinking Violet computer genius Yukino Kikukawa. This is more or less reinforced by the fact that both her Child and her Element are only good for detection and spying.
Zelgadis Graywords of the Slayers franchise is usually this alone or is also The Lancer, depending on the adaptation. In addition to being book-smart and a strategist in battle, he also knows a good deal of scientific knowledge plausible for a fantasy setting, and can solve math problems and measure distances at near-breakneck speed.
A more straightforward smart guy is Xellos; however, he subverts this trope by being the Token Evil Teammate that just so happens to be a part of an Always Chaotic Evil race of demons, so naturally, he rarely, if ever, explains anything.
As a member of the Magician's Guild, she admits to being a novice, but makes up for it with her extensive knowledge of magical artifacts and ancient tomes, which she uses to help Louie and his friends.
In the 15th episode, she fares better against the 'Guardian of the Lake' than the rest of the group: first she flushed it into the open by using the depth charges she made. Then managed to temporarily stun it by using her "shock box" to generate a high voltage current through the lake (seen from 14:51-16:03).
"G-4" Jinpei the Swallow from Science Ninja Team Gatchaman fills this role in the "smartass" variation of this trope. He's a Tagalong Kid who is the most prone to clever trickster style behavior and wisecracking. He often hangs out with and plays off of The Big Guy Ryu the Owl for his hijinks. As far as actually being the book smartest member, his sister Jun better fulfills that role. Jinpei and Jun split gadgeteering skills between them.
Other characters could also be considered for the role, such as Asakura, who is an expert at gathering information, and Haruna, who usually comes up with the devious plots. Other characters, such as Chachamaru and even Negi himself have gone into this role.
Subverted in Haruhi Suzumiya, where Yuki Nagato is designated by Haruhi as The Smart Girl. The real smart guy is actually Koizumi, constantly giving advice to Kyon in any way, while Yuki is much more of The Big Guy, being essentially the Brigades' super powerful member.
Kurama in YuYu Hakusho rarely fights hand-to-hand and never wins through brute strength; he always has to take his time to devise a strategy to beat his opponent. (This is Lampshaded several times and gets him in trouble more than once.)
Fate herself fits this role in any The Team or Five-Man Band constellation with Hayate as The Leader, since Fate is an Enforcer who investigates crime incidents. Also temporarily in Force, when she, Nanoha, Isis, Subaru and Lily fight Thoma, who lost control over his body, Fate makes the smartest move to end the battle very quickly.
Teana fills this role in the third season, being recruited into Riot Force 6 for her skills as a tactician, a role that she eventually lives up to in spades. She is also The Leader of the Forward Team.
In ViVid, Corona is The Smart Girl of Team Nakajima, who uses various strategies and she copies the moves of her teammates by programming them into her Golem.
In several of the Sonic continuities (bar the animated SatAM and Sonic the Comic series), Tails usually plays this role.
Christopher Thorndyke plays this role in the Sonic X series after his six year age up this caused a bit of conflict amongst fans, and Tails becomes more of a Captain for the crew (albeit one who is not always listened to, but he is trying to organize Amy Rose, Knuckles and Sonic) and a mechanic.
Among The AlliedForces, Francis Bonnefoy aka France takes up this role. He's one really atypical Smart Guy, though, often thinking with the smaller head rather than the big one. But when he does use the latter rather than the former, he can be quite the Manipulative Bastard.
Usopp from One Piece fills this role for the Straw Hat Pirates. Initially, it is arguable that Nami is the smart guy and Usopp is the chick due to both of them being smart (in different areas), but with Usopp being better in battle. However by the time Enies Lobby arrives, they are both capable combatants (though among the crew, they are the least reliant on physical abilities). Despite Oda officially stating Nami to be smarter than Usopp, taking into account his higher bounty, his ability to analyze his opponents' fighting styles, and his uncanny ability to think five steps ahead, Usopp is clearly a straighter Smart Guy when it comes to combat situations, though they both contribute intelligence in non-combat situations. Also, he is a Gadgeteer Genius who built Nami's weapon (at her request, meaning she couldn't do it herself). When it comes to more conventional sciences, Nami has him beat, but in the world of One Piece, conventional sciences are rarely applicable.
Nico Robin is the smartest person in the crew, being a historican and archeologist she knows more about the world when anyone and she judges situations right.
Sanji's also proven to be capable of planning some impressive strategies as well, like the whole "Mr. Prince" ploy at Alabasta to lure Crocodile out of his casino and rescue the Straw Hats that were trapped inside in a sea prism stone cage. He's definitely the smartest of the Straw Hats' "Monster Trio." Unfortunately, his brains tend to go right out the window if women are involved.
Sanji tends more to be the Lancer or the Big Guy (with women involved) since he is the almost perfect counterpart to Luffy. He thinks first, watches his speech and he can cook.
Quite surprisingly to all those who've known him for a short time, Gokudera from Katekyo Hitman Reborn!. Why surprisingly? Because the guy is the essence of a bad boy, smoking at the age of 14, ready to beat up a teacher if his boss say so, etc., while getting 100 on his tests all the time. Not to mention his C.A.I system and making up his own alphabet in class out of boredom...Rarely acts like one though.
Shikamaru is certainly the series' smart guy in the sense that he has a brilliant strategic brain and improbably high IQ and a talent for utilising humiliatingly complex and cruel gambits. When he can be bothered to.
Sakura is a straighter example for Team 7 in the early part of the series. Should couldn't fight but perfectly understood how every technique and strategy works. She was also one of the few people smart enough to answer the questions the written exam without cheating.
In the later part of the series Kakashi transitions from being a Lightning BruiserMentor into being the Smart Guy when the others start to catch up to him in power, and the others catch up to Sakura in technical knowledge.
Practically everybody transforms into this during a battle.
In Digimon Adventure, Izzy would qualify as "The Smart Guy". As well as Ken in Digimon Adventure 02. They are geniuses after all.
Don't forget Yolei/Miyako in Digimon Adventure 02. She held this position prior to Ken joining the heroes and shared it with him afterwords.
It isn't long before she becomes the brains of Takashi' group, with the others often deferring to herto assess the situation and devise a plan of action. In short: what she lacks in combat skill, is more than amply made up for in intellect, which has saved their lives on more than one occasion.
Kabuto from Psyren, of the street kind. He also happens to be a Reality Warper, so he's useful on the battlefield now, too.
Sailor Moon's Sailor Mercury/Ami Mizuno has an extremely high IQ, is Japan's unrivaled best student, is the most studious, and her uniform is equipped with an instrument for analyzing enemies. Her brains are pitted against Sailor Uranus's brawn in the Sailor Stars, and she defeats the enemy by studying them and using observational skill rather than simply trying overpower them, thereby winning Uranus's respect.