There is a big probability that huge Zelda Spoilers are ahead. If you do not want one or more of the Zelda Games to be spoiled for you, leave now!
As many of you know, the Zelda games go in some sort of order, and Nintendo has a big ol' document that links them all together. Sadly though, Nintendo doesn't explain much what order they go in. So, what order do YOU think they go in? Firstly, here are parts of the order that Nintendo confirmed and a chart explaining what each abbreviation means. Please use these abbreviations when you are posting what order you think the Zelda Games go in.
Legend of Zelda = LoZ
Zelda 2: Adventure of Link = AoL
Legend of Zelda: A Link to the Past = Alttp
Legend of Zelda: Link's Awakening = LA
Legend of Zelda: Oracle of Ages = OoA
Legend of Zelda: Oracle of Seasons = OoS
Legend of Zelda: Ocarina of Time = OoT
Legend of Zelda: Majora's Mask = MM
Legend of Zelda: Wind Waker = WW
Legend of Zelda: Minish Cap = MC
Legend of Zelda: Four Swords = FS
Legend of Zelda: Four Swords Adventures = FSA
Legend of Zelda: Twilight Princess = TP
Legend of Zelda: Phantom Hourglass = PH
The following chart (Which is a chart showing the confirmed pieces of the order by Nintendo) goes from left to right. When there are two games in one section, that means they happened at the same time. If there are two games in one section and a question mark in between them, that means that we don't know if they happened at the same time or not.
Alttp > LA ? LoZ > AoL
Notes: In the manual of Link's Awakening, it states that Link's Awakening comes after A Link to the Past in some way or another. Nintendo said a while ago though that A Link to the Past comes before the Legend of Zelda 1. Whether or not LA and LoZ at the same time or not is yet to be confirmed (as far as I know). Also, Adventure of Link takes place right after the Legend of Zelda 1. Link apparently defeated Ganon, and Zelda falls under a spell. Once Zelda falls under the sleeping spell, you go out looking for the cure. But Ganon's minions want Ganon to be revived, so they go out lookin' for ya. Thanks for the Action Game/RPG excuse, Nintendo! >=/
OoT > MM ? TP > WW > PH
Notes: As we all probably know, Majora's Mask is a direct sequel to Ocarina of Time. Link goes out to find Navi, blah blah. The Wind Waker also makes very clear references to Ocarina of Time. However, both games speak of OoT in a different way. Majora's Mask speaks as though Link and Zelda actually made sure that Ganon never obtained the Triforce of Power. The Wind Waker speaks as though Ganon did obtain the Triforce of Power, and that he managed to rule the land for 7 years until Link stopped him. Right after Link stopped him, he was sent back in time by Zelda, in an attempt to make sure that Ganon never obtained the Triforce of Power. Confusing, is it not? This is why I, and many others believe that a second time-line was made afterwards. Now onto a different subject in the Zelda matter, Nintendo has stated that Twilight Princess comes in-between Ocarina of Time and the Wind Waker, so this is going to be before the flood. While we don't know if it happens at the same time as Majora's Mask or not, it's a safe bet that it comes after, as Nintendo has said it (TP) could be decades after OoT, while in Majora's Mask, the Link of OoT is still just a kid. On a side-note, Nintendo has said that Phantom Hourglass comes after the Wind Waker.
Sadly, I do not know the confirmed order for any more of the games. If someone could post a link confirming more as far as the timeline in Zelda goes, it would be greatly appreciated.
Keep in mind that these lists can enter the other lists in any order depending on how Nintendo pleases. That's why it's so hard to find out which games come after which games. >_< Anyway, what order do you think they go in? I haven't come up with a full theory yet, but I think that FSA comes up some time after Majora's Mask. I say this because in Ocarina of Time (Adult Version), Ganondorf gets his power from the Triforce of Power. In the Child Version of OoT, however, he does not. Majora's Mask takes place in the child time-line. In Four Swords Adventures, Ganondorf never obtains the Triforce of Power. All he gets is a cool Trident. The... >_> TRIDENT OF POWER!!!
Edit: Ah, this link here confirms that two time-lines exist. n.n Just thought I'd note that part.
http://www.zeldalegends.net/index.php?p=233&style=twwQ: Where does The Wind Waker fit into the overall Zelda series timeline?
Aonuma: You can think of this game as taking place over a hundred years after Ocarina of Time. You can tell this from the opening story, and there are references to things from Ocarina located throughout the game as well.
Miyamoto: Well, wait, which point does the hundred years start from?
Aonuma: From the end.
Miyamoto: No, I mean, as a child or as a...
Aonuma: Oh, right, let me elaborate on that. Ocarina of Time basically has two endings of sorts; one has Link as a child and the other has him as an adult. This game, The Wind Waker, takes place a hundred years* after the adult Link defeats Ganon at the end of Ocarina.
Miyamoto: This is pretty confusing for us, too. (laughs) So be careful.
Start thinking... NOW!!!