1. The Architect, in the Matrix series
Apparently the Architect has helped create the Matrix, which means he's a Machine, or maybe an avatar of a Machine. When he explains to Neo what's happened with all the versions of the Matrix, it's pure wizard territory: an infodump wrapped in a riddle wrapped in a white beard. He's not really a god, though he seems to have godlike powers that make no sense. He's the closest thing that the Matrix has to Sauron, and given the mystical underpinnings of this series it's no wonder that a wizardy guy lurks at the heart of the computer system.

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2. Henry Deacon on Eureka
Though Eureka is one of those shows that takes some pains to make its science plausible, it is also unquestionably the story of an enchanted town in the middle of a Muggle world. Yes, the "enchantment" comes from government money allocated for weird science, but the science is often so implausible (parallel time lines?) that Eureka sometimes seems one step away from becoming Hogwarts with quantum computers. At the heart of this science fairy tale is Henry, a genius who would rather live in a garage than a laboratory. His cryptic knowledge, seemingly limitless abilities to bend space and time, and his often odd behavior make him more Dumbledore than mad scientist.

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3. The Doctor
Yes, the protagonist in Doctor Who is an alien from another time, but (as characters often remark) he has a magic box. Not to mention a magic screwdriver, magic paper, and the kinds of outfits more befitting a wizard than an alien. Seriously - what kind of alien wears celery as a stickpin? That is sartorial sorcery, people.

4. The Dixie Flatline, from Neuromancer by William Gibson
A dead hacker whose brain has been saved onto some ROM that our hacker hero Case manages to rescue. From beyond the grave, Dixie helps Case on his mission and dispenses the kind of wisdom you expect from a being who is essentially a supernatural figure, a digital ghost. Dixie also consorts with other higher beings, A.I., that the humans can't really understand. He's a high tech magic user in cyberspace.

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5. Q in Star Trek: The Next Generation
Yeah, yeah extra-dimensional entity from the Q Continuum, which could exist if you believe in some weird version of string theory. Face it: Q is a wizard. He's got the whole "let's test humans using strange pig creatures while wearing flowing red robes" thing going on. He can change reality with the snap of his fingers. His powers come from whateverness. Let's just admit the guy is magic and move on.

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6. Yoda and/or Obi Wan Kenobi from Star Wars
People often opine that Star Wars is actually a fantasy series due to its many non-scientific touches, up to an including midichlorians. But I would contend that Star Wars is definitely science fiction — just packed with fantasy characters, such as wizards. Yoda would be my first choice for a wizard character, due to the cryptic comments and "teaching the humans using strange lessons" aspects of his character. But Obi Wan Kenobi runs a close second in the wizard department, especially once he dies and goes Dixie Flatline on Luke's ass, dispensing wisdom from beyond the grave.

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7. Jonathan Strange and Mr. Norrell, from the eponymous novel by Susanna Clarke
This is an odd choice, but hear me out. Yes, Clarke's novel Jonathan Strange & Mr. Norrell is entirely about wizards (and faeries) who use magic, and there is no science fictional setting. But our two protagonists manage to resurrect magical powers that haven't been seen in England for generations using what amounts to scientific and scholarly methods. In the novel, magic is a combination of book learning and practical application. Nobody has practiced magic for centuries because it has become a kind of antiquarian study — until Strange and Norrell come along. Set during the early nineteenth century, at the dawn of the industrial age, the book seems to suggest that wizardry is a form of science or perhaps engineering that is becoming acceptable again as magicians begin to embrace the scientific method. One could make a similar argument about how magic works in a lot of China Miéville's novels too, most notably the Bas Lag series.

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8. Wizard Shazam, DC Universe
Comic books are packed with wizards who co-exist with a bunch of science heroes. Indeed, some science heroes even get their powers from wizards, as is the case with the Wizard Shazam, who gives Captain Marvel his powers — which he uses to fight a mad scientist, among other enemies. So you've got wizard powers vs. science powers all in one place! After Captain Marvel and his Marvel Family lost popularity, DC tried to revive the character by making his wizard mentor more prominent, in a series of Shazam books and cartoons. Other wizards appear in DC, like Dr. Fate and the Phantom Stranger. In the Marvel universe, there's Doctor Strange. And there are probably dozens more.

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9. Turjan, The Dying Earth, by Jack Vance
In Jack Vance's series of connected stories and novels about a far-future Earth, the sun is dying and people no longer understand the difference between science and magic. The planet is populated by wizards who gain their powers, like Jonathan Strange and Mr. Norell, by reading books and traveling to seemingly supernatural realms to gain knowledge. One of the "good" wizards is called Turjan, who owns books containing the few spells that humans can still cast (there were once thousands, but that knowledge has gone). Turjan fights bad wizards, and often casts spells that seem like they might also be commands that execute programs using some kind of hyper-advanced, post-singularity device. Some might say Vance, who wrote in the mid-twentieth century, was the first scifi author to really explore how you could plausibly have wizards in a scifi scenario.

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House from the TV series House
This choice may also seem like a bit of a stretch, but I think House — like Henry on Eureka — is one of those science characters who hovers right on the edge of being a wizard. He seems to be almost magically powerful, using improbably advanced tech sometimes (c'mon - the machine that reads dreams?), and he shares with most wizards a quixotic and tricksterish nature. With his snark and misanthropy, House is a real-world version of Merlin from Excalibur — he even carries a wizarding staff in the form of his cane.