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I'm really not sure about the exact nature of the Zelda timeline, and the creators themselves have said that though they have outlined it, they keep it secret. Whether or not they plan to reveal it is unknown.

We do know some things for certain. It has been confirmed that until Skyward Sword came into production, Ocarina of Time was the very first series of events to take place in the LoZ timeline. You are correct in saying that there was a split in times/worlds after Ocarina of Time (at least as far as we know), as the Wind Waker and Twilight Princess universes have been confirmed to be related, but separate. For Wind Waker's timeline, there was a great flood sometime after Ganondorf was defeated in OoT (confirmed in WW's intro), and Hyrule sank beneath the Great Ocean, leaving only a few islands remaining, "the legend of the hero traveling on the breath of the wind..." or something like that. For TP's timeline the flood never happened (obviously), and we continued through the series to reach a Hyrule that clashed against the Twilight Realm, which I'm not sure exists in both universes (although I think that it does).

Eiji Aonuma has confirmed that Skyward Sword comes before Ocarina of Time, actually. We know this to be true because the game will be addressing the creation of the Master Sword itself, so it automatically precedes any game that has the Master Sword in it.

Confirmation here --> http://gonintendo.com/viewstory.php?id=130953
and --> http://www.escapistmagazine.com/news/view/102262-Nintendo-Places-Skyward-Sword-in-Zelda-Timeline

We also know that Wind Waker is indeed followed by Phantom Hourglass, which in turn is followed by Spirit Tracks (confirmed by the games themselves as direct sequels of each other).

As for any other details of the timeline, we can always speculate. We know Skyward Sword and Ocarina are the first two in the series (for now - the creators have also stated that the timeline is kept secret and flexible because they don't want it to be limiting ideas for future games).

So yeah. I hope this helps you a bit. It's always fun to theorize and it helps that we do have some confirmed facts XD

I tried to comprehend the Zelda Timeline once.

My brain exploded. XP

There is a good possiblity that WW, PH, ST come more towards the begining of the timeline, most likely after TP, but wouldn't the legends told say something about a boy who could turn into a wolf, or mention something about the Blue Eye-beast?

TP comes after OoT. What supports this for me: In TP, at the finshing pond, when you look at the pictures she has on the wall. Notice one of them is the fisherman from OoT. After a moment of looking at it, if I am not correct, she addreses the picture to be her grandfather (or great grandfather one), the greatest fisherman to live. Putting TP shortly after OoT. The childern, grandchildren, more likely great grandchildren of Zelda and Link. In TP through out your journy, you awaken the hero inside of you, with the warrior's sprit. Who is this guy? I don't remeber how he introduces himself, but could he possibly be Link's sprit?.... Coming back to help after he left Hyrule?

In WW, The Old Land that used to be know was flooded due to the return of Ganon. The reason of the Gods flooding the land was because Link had left, and never came back. Now this somewhat hints that OoT came before. MM follows OoT. MM can explain what happened to Link after Zelda sends him back to his childhood at the end of OoT. Now, MM mask doesn't take place in Hyrule. It takes place in Termina. Hince The WW legend saying that the Hero of time left and never returned. Maybe something happened to Link before he returned to Hyrule, form Termina? (Refering back to the Sprit warrior.)

Something else for us to ponder on, The Old Land of Hyrule was flooded. Why? Because of the return of Ganon and the lacking of the hero. They explain though that the young boys on Outset Island, once they came of age they would dress like the legendary hero. The explain it as a write of passage. Maybe this used to be some sort of thing they did to find the hero. Find his liniage and such. Then obver time it must have died out, and turned into tradition.
In WW, they never addressed the playing map to no certain place. It was just an ocean with a couple of islands. It would never let you sail out of the area. (Curse you limited memory game making shishkabobs! XD) At the end of WW, Tetra and Link saild off "to find a newland of Hyrule". Now in PH we're still with Tetra, sailing on that nameless ocean. Making PH pick up right after WW. Tetra gets "kidnaped" by the Ghost Ship, from WW. Of which *spoiler* turns out to only a 10 minute nightmare....basiclly.