The idea that all of the Legend of Zelda games take place in the same universe (or a pair of parallel universes) along some mysterious timeline has been floating around for a bit, but Nintendo has only given out hints about the nature of it. Talking to Zelda Dungeon, Localization Manager Dan Owsen reveals that at one point, some employees wanted to help settle the debate once and for all by posting the correct order online, only to have Nintendo of Japan shut down that idea. Their reasoning was essentially that players should have the freedom to interpret events their own way, and that posting a definitive answer would stifle their imaginations.
I can't really blame Nintendo for not wanting to spill. With the idea that two different parallel universes spawned from all the time traveling in Ocarina of Time, explaining the situation could make the game sound like an episode of Fringe and not a fun fantasy adventure.
As for where the next new Zelda game fits in, there are rumors that Skyward Sword will be, chronologically, the first game in the series, although Miyamoto has only confirmed that it's set before Ocarina of Time. I'm sure there will be some awesome internet arguments about it once the game is out later this year.
Exclusive Interview: Dan Owsen Talks Zelda Timeline [Zelda Dungeon]