Think Twins

Twins are often treated as the "thinking engine" who come up with plans (be those devious or truly smart) because, well, there are two of them, and they are on the same wavelength (more so than just regular friends) so they can come up with things among the two of them more effectively than other two characters, which would involve a lot more explaining yourself and arguing.

Putting these guys on Mission Control is also quite logical - often you need to show that technical equipment takes more than one person to operate, but both people essentially do the same task, and it would be a waste to characterize separately two people who essentially fulfill the same role on the team (or, on the other end, sacrifice two interesting characters to do one job).

May overlap with Trickster Twins.

Anime and Manga

 * From the manga Project ARMS, there are Al and Jeff Bowen, evil genius identical twins, and also Katusmi and Kei, who are identical female twins; Kei's The Chick, and Katsumi's a Damsel in Distress and a major plot point.

Film - Animation

 * 3 and 4 from Nine, also Single-Minded Twins (and, if it means anything, mute).

Film - Live Action

 * The twins in Men in Black

Literature

 * Fred and George Weasley from Harry Potter, even though they're more Trickster Twins, it did take a certain amount of brain power to make all the Weasley Wizard Wheezes.
 * Beltira and Belkira of the Belgariad and Malloreon. They spend most of their time in the Vale of Aldur trying to decipher a multitude of complex prophecies, while the other sorcerers act on what little information they can find.

Live Action TV

 * Power Rangers RPM had genius twins Gem and Gemma.
 * The Edison Twins.
 * The Bynars from Star Trek the Next Generation are an entire alien species of Think Twins.

Western Animation

 * Doug: Al and Moo Sleech
 * Detention: Orangejella and Lemonjella LaBelle
 * The "tweebs" from Kim Possible. Granted, everyone in the Possible family is a genius, but the twins are significantly smarter than their older sister. And also twelve. And in high school.
 * Johnny Test: Susan and Mary Test.
 * A set of overachiever twins seen in one episode of Static Shock.
 * Thunder Cats had Wily Kit and Wily Kat, who, as their names suggest, were quite wily. Lion-O had to face the pair of them to overcome the Trial of Cunning.
 * The Platypus Brothers from Taz Mania.