Interesting discussions going on here!
First, I think Ovyovyoyv or however one spells that has written down exactly my thoughts about Phantom Hourglass, what he wrote is also what I don't like about that game.
Now to talk about timelines... I think the two timelines theory is rubbish, either you can link the games somehow or you can't is my opinion, but creating multiple timelines is not really my thing.
It's been quite a while since I've last played a Zelda game, so I don't have all the facts of the plots present currently, but I try to write down my thoughts anyway.
It is clear to me that there must be several different Links - I guess we all agree on that. Still, there are some games in which we see the same Link again, the direct sequels.
Direct sequels are, in my opinion:
TLoZ: Link's Awakening to TLoZ: A Link to the Past
TLoZ: Majora's Mask to TLoZ: Ocarina of Time
TLoZ: Phantom Hourglass to TLoZ: The Wind Waker
I'm not sure about that one, but I think Link's Adventure is also a direct sequel to The Legend of Zelda. Am I right?
Also, the two Oracle games are also sequels, but it's debatable to which game their are. They have to be because the Link in those games is an already proven hero. I think it's either a sequel to Link's Awakening or to Majora's Mask, but I'm not sure what Link does at the end of those games and if a sequel for those would be possible.
So this actually makes it six Links. Here are the games they first starred in:
Legend of Zelda
A Link to The Past
Ocarina of Time
The Wind Waker
The Minish Cap
Twilight Princess
In all of those games, a normal boy becomes a hero, while in the others, Link already is one. So all we have to do now is sort those games.
I think Ocarina of Time is really the one that starts everything, there is no mentioning of any previous events in the game and in the manual, there are also things written about the creation of the world, so this clearly is number 1 for me.
Now it gets difficult since I don't remember all the plots. I think though the next one which I'd put here is Legend of Zelda. I have forgotten what makes me think that way though.
After that, we either have the "water games" starting with Wind Waker or we have Minish Cap... I really don't remember which would fit better first though. However, I think they are 3 and 4 respectively, I just don't know in which order.
After that, I put Twilight Princess. I don't know how that water could vanish again, but if it can come from somewhere, it can also disappear, right? So this is my number 5.
The last one should be A Link to the Past. I think that was also stated by someone at Nintendo sometimes (don't remember if it was eji or shigeru though...) and it also makes sense since there's a lot of back stories in the game, and it definitely plays after Ocarina of Time because of the sages thing. Also, I feel that Twilight Princess is a prequel to ALttP because of the whole parallel worlds thing. This is also the reason why I put Twilight Princess after Wind Waker.
These are my thoughts summed up. Whar are your opinions about them?