Ah, floating landmarks. Chances are, if you're playing an RPG, you're probably gonna run into at least one of these oddities--some castle, temple, town, or entire island which just hovers miles above the rest of the planet, sometimes for an explained reason (usually involving magic or technology so crazy it might as well be magic), and sometimes just because it apparently can. Not only is it a convenient setting for bad guys' HQs, highly advanced cultures, and mystical descendants whose ancient ancestors have passed down the secret arts of creating important plot points and twists, but it also provides more game-lengthening material in the form of quests to obtain the means to actually get up to these floating landmasses in the first place.
It's not like this is just a modern aspect of RPGs, either. Floating landmarks are one of the oldest consistently-used traditions RPGs have. Zeal in Chrono Trigger, the Sinistrals' island in the Lufia series, Golbez's tower in Final Fantasy 4, the Mana Fortress in Secret of Mana...I mean, Crystalis for the NES had a floating tower filled with ancient and forbidden technology. Crystalis. I remember having a question I asked about Crystalis's ice mountains published in an issue of GamePlayers back when I was in 3rd grade. I'm 23 now. And the game had been out for a long while by the that time, too. That's how far back you can find magical floating places in RPGs.
Hell, there's a floating castle in Phantasy Star 1. Back on the Sega Master System. 1987. It's seen more years than probably about half of the people on this forum have.
Since you see it a lot in anime, I'm guessing that it must just be a Japanese thing (though Secret of Evermore, a US-made title, had a futuristic city in the sky, too). It's a really strange cliche, though, when you think about it. I mean, it's not like we have anything remotely like it here on Earth to use as a reference. The closest we really have are large airplanes which can carry several dozen people for extended periods of time, but those still have to land and refuel, not to mention get maintenance, pretty frequently when compared to some RPG's mystical floating castle that's been hanging out in the sky for the last 1000 years.
What's even stranger is that it's a cliche that RPG fans by now seem to generally accept unquestioningly. I mean, here we are, being told that somehow, somebody on this technologically backwards little planet where the idea of a steam engine is cutting-edge technology had the knowledge and ability millenia before the game begins to construct a massive floating building that's more than likely equipped with more laser beams of doom and robot guards than the Technodrome, and we just take it in stride, not once considering the possibility that this is absolutely ludicrous even by the standards of a game where you can do more damage with a pointed stick than a bomb blast can if you just have a high enough number next to the section of your Status screen that says Strength.
The concept's given way to some really neat and innovative ideas in a few games, though. Not so much in its usual form of one large amount of land floating around for no good reason, but rather, in the form of a world comprised of nothing BUT floating islands. It's an exceptionally strange and interesting world idea that's surprisingly been found several times in RPGs--Bahamut Lagoon, Skies of Arcadia, and Baten Kaitos are all RPGs taking place on worlds made up of giant sky islands (or lagoons, as the first calls them) inhabited by people who use various forms of transportation to travel between the islands, be they sky-faring animals like dragons (Baten Kaitos), ships resembling Earth pirate vessels and military battleships (Skies of Arcadia), or even smaller floating islands which are fitted with engines and have a ship's interior constructed within them (Bahamut Lagoon--it's a seriously neat idea, in my opinion). The result of this exceptionally bizarre setting is almost always a very interesting and innovative story.
But yeah, anyways, just really hit me today exactly how frequent and traditional the whole idea is in the genre, and I thought I'd make note of it.