Ok, seems people are behind on the Zelda Lore
Ocarina of Time Link - The very first Link, this game talks about the creation of Hyrule and the Tri-Force, it is mentioned in LTTP that Ganon was once a thief named Ganondorf who stole a piece of the Tri-Force. Which is the event in OoT. Link (Hero of Time, original) travels back and forth in time to prevent the future that is Ganon. He prevents any of the events of OoT from ever happening.
Majora's Mask - Link, Hero of Time, having altered the fate of the world, goes to search for Navi, his farie companion from the OoT. Random adventures afterwards. Nothing is known about the fate of Link after this. This Link hasn't been featured in any other games besides Smash Bros. and Soul Calibur 2. (Story Unrelated)
Twilight Princess - This is the alternate future of Hyrule, Ganondorf never gets to steal a piece of the Triforce. This is why the world is all mixed up from the OoT world. It's because it's an alternate future. Ganondorf is sealed in the Twilight Realm by the Sages, who are different from the OoT sages, because of the alternate timeline. He is destined to have the Triforce so he gets the divine power while he's about to be killed. This Link, I like to call him Feral Link, isn't recognized as a hero, because he turns into a wolf, and he has to keep low Key. Also, the people don't seem to remember ever getting transformed into spirits. Which is a good referance to the next game in the timeline.
Wind Waker - The Great Flood occurs, the old world of Hyrule was flooded. There wasn't a "Hero of Time" to reincarnate to save them, as the problem most likely had nothing to do with the Triforce, which is generally the only reason Link appears. (Other games are sidequests.) Ganondorf gets a piece of the triforce, so does link. Ganon loses it and fights link sword to sword. Link defeats Ganon. This is Link III.
Phantom Hourglass - New Hyrule is found?
Legend of Zelda - Link gathers the piece of the triforce is wisdom and defeats Ganon.
Adventure of Link - Events of Z2 take place, I haven't played it. this is the fourth Link. Same one from the first game.
Link to the Past - The last game in the Triforce - Ganon - Zelda - Link timeline. This Link is the decendant that Ganondorf speaks of exterminating from OoT. Since this Link is said to have a certain lineage. This game mentions the origins of Ganon, being the events from Oot. This is the new Hyrule that Link and Tetra find. Ganon gets the entire triforce, the master sword is still in the forest (The Ruins of the Temple of Time, from OoT and TP) and there are no ruins at all. Ganon creates an alternate world with the power of the whole triforce. Ganon is at his strongest here since he has the whole triforce. Link defeats Ganon at full strength, ganon is finally shown dying. And Link gets the whole triforces and turns to world into the golden land, and it is prosperous for eternity. Link returns the master sword, and it says that The Master Sword rests forever, not stated in the previous games (I don't think). This is link V.
Link's Awakening - This is the same Link from LTTP, says Miyamoto. All a dream.
As for OoA and OoS, I wouldn't know.
As far as the timetravel stuff. I don't like to get into that too much, it makes me think a lot. OoT events are key to the timeline. But the timeline doesn't really fit together that well, so people seem to make things up.
All I can say is that I think a Hero is predestined to save Hyrule, or find it. They are garbed in Green (in tradition of the Hero of Time) and there names are all Link coincodintally.
My Favorite Link is TP link, he's more personal, he has friends and he's on a mission to rescue them, THEN he realizes it's his responsibility to do more.
Midna = Best Side Kick Evar.