Steve Jackson Games has already done GURPS: Cthulhupunk, a sourcebook that puts Cthulhu IN CYBERPUNK!
And for the BRP system of and a Chaosium-licensed product, there's Cthulhu Rising - the original Call of CthulhuIN THE FUTURE! AND IN SPACE! BATTLING DEEP ONES ON EUROPA! RUNNING FROM DIMENSIONAL SHAMBLERS ON GANYMEDE!
d20 Future is d20 Modern (which is Dungeons & DragonsIN THE MODERN WORLD!) IN THE FUTURE!... oh, all right: IN SPAAAAAAAAAAAAAACE!
d20 Past and d20 Apocalypse are Dungeons & DragonsIN THE LATE 1800s and AFTER THE END respectively. Both also have Urban Arcana style settings.
TravellerIntersteller Wars is the Greco-Persian wars in space, all the way from Marathon through Alexander's conquest.
Warhammer 40,000 began as WarhammerIN SPACE! but is now pretty much its own entity; it still, however, has goblins in space, orcs in space, elves in space, ogres in space, the Church Militant in space, vikings in space, communists in space and Chaos Gods in space. Previous versions also had dwarfs in space.
Mage: The Ascension was originally conceived as the medieval RPG, Ars Magica, IN THE MODERN DAY! — but then begat not only Mage: The Sorcerers' Crusade (MtAIN THE RENAISSANCE!), but, once White Wolf sold the rights to Ars Magica itself, Dark Ages: Mage.
Exalted, in turn, was supposed to be the original Old World of DarknessIN PREHISTORY! — but then came Scion, self-described as Exalted: IN THE MODERN WORLD WITH ANCIENT MYTHS ON TOP! (Though Scion doesn't necessarily match that description.)
With Shards of the Exalted Dream, Exalted has two different variants of ExaltedIN SPAAAAAAAAAAACE! No, seriously. The cover even has the Scarlet Empress doing her best impression of a certain Spectre, plus another version who's a space barbarian queen with autoklaves behind her throne. The two variants are Heaven's Reach, which plays space for grandeur and size, and Gunstar Autochthonia, which is a lot more claustrophobic. Shards also includes The Modern Age, Exalted in a modern setting, and Burn Legend, which is basically Exalted as a video fighting game.
Scion itself has a couple of alternate settings: the campaign in Scion: Ragnarok takes place in a setting where only Norse Mythology is true, as opposed to the basic Scion setting where All Myths Are True, and Scion Companion offers a historical setting in World War II.
There are also the settings in different cultures. Best known is the Year of the Lotus event which gave Asian treatments of every gameline, the flagship title being Kindred of the East.
The New World of Darkness has two types of alternate setting: one, nicknamed "Shards", translates the NWOD into alternate genre-settings, such as Bleeding Edge, which is NWOD cyberpunk, and Infinite Macabre, which is the NWOD IN SPACE! The other is historical settings for the various gamelines, such as Requiem for Rome, which is Vampire: The Requiem in the dying days of the Roman Empire, and Victorian Lost, which is Changeling: The Lost in Victorian Britain. Mage Noir manages to pull off a two-for-one, being Mage: The Awakening in the noir genre, set in post-World War II America.