Blackberry, of the initial refugee band in Watership Down. An amusing variant in that his skillset is basically that of an engineer, except downsized to a rabbit POV; his bright idea — which becomes the key strategem in the climactic battle — is that things which float on water can thus be used as transport out of reach of land-based enemies. It's strongly hinted that Fiver, the small seer who doesn't fight, is second smartest.
Deconstructed in the Warhammer 40,000: Eisenhorn novel trilogy, where the savant Ueber Aemos is the walking databank he is because of a "meme-virus" that makes him compulsively pursue knowledge, culminating in memorising the Malus Codicum.
Hermione Granger. It's a Running Gag that she's the only one of her friends (and one of few in the entire school) who actually read "Hogwarts: A History", making her Ms Exposition. Harry and Ron have increasingly snarky responses to her exasperation at no-one else reading it. More seriously, she's also extremely intelligent and logical, and she's the best at magic of the three, frequently performing very complicated spells for someone her age.
Dumbledore lampshades that since he's regarded as this, his mistakes are that much greater when he screws up (which isn't very often, but massively sucks when he does). He also admits he subverts this trope a lot, because a lot of his genius (in regards to the plot) is actually a bunch of educated guesses (read Half Blood Prince for full details).
Remus Lupin is this to the Marauders, a slight variation being that he is book smart as opposed to the Brilliant, but Lazy James and Sirius.
Ax, because he's an Andalite and therefore knows a lot more about science.
While there is no clear Five-Man Band at any point in The Heritage of Shannara, The Smart Guy is probably Morgan Leah. He seems to be the automatic go to for strategy and sneaky plans, regularly divising ideas to get the Free-born in and out of Federation jails, cities, and fortresses. Walker Boh could also be said to fullfill this role, as the resident Druid. Both are far from weak or stereotypically geeky.
Also the Lucians in their own scheming way.
Mention must be made of polymath, weapon-maker (and namer), Perky Goth, occasional Amazon and all-around bright girl Dess (Desdsemona, in full) of the midnighters trilogy. You've never met anyone as good at maths - or at applying it - as Dess.
Thomas from Malevil. He's a college educated student of science in a rural region of France. Skeptical and an atheist to boot.
Harry Dresden seems to be this to his allies - not because he's much smarter than his friends, but because he's often the only guy who knows what's going on. He starts to share information with his allies after making a bunch of mistakes that still haunt him, and this effect decreases to some extent.
There's an excellent case for Bob the Skull being this to Harry, because of his vast degree of knowledge.
Beetle in Septimus Heap. While lacking both Septimus's Magykal powers and Jenna's speed, he's quite versed in knowledge of Magyk and other arcane matters.
In Galaxy of Fear, DV-9 starts off in this kind of role, though all characters tend to know or be familiar with something that the others don't, and even Book Dumb Zak is fairly intelligent. By the end of the series, while Uncle Hoole knows more in general this role is largely taken by Tash, who is studious and tends to think more and plan, compared to Zak who does more reacting.
X-Wing Series: While most members of Wraith Squadron are smart in their own way, Voort "Piggy" saBinring takes the cake in terms of sheer intellectual ability. He can calculate hyperspace routes in his head, coordinates dogfights while in the middle of them, and when taking over command of the Wraiths, he came up with a perfect plan to bring down a corrupt general that impressed Face Loran himself. The kicker? He's a Gamorrean.
Laeshana, from The Quest of the Unaligned is brilliant even for an aesh. At the beginning of the story, she suspects that the theory of magic everyone's followed for the past 800 years is missing some major parts. By the end of the story, she's proven right.
Beetee in Catching Fire and Mockingjay, especially because he's from District 3, which makes electronics and explosives.
Lissa Dragomir has excellent and consistently high grades. She later uses her intellect to investigate a regicide and simultaneously work on the mental challenges presented to candidates in the running to become the Moroi monarch. She does well on both fronts.
Sydney Sage is multilingual, a car geek, interested in classical architecture, skilled in using computers. All as a teenager.
In the Rainbow Magic movie, Sunny/Saffron is this; she's very smart and analytical.