The "true" timeline is that Ganondorf conquers Hyrule. This is the main timeline.
However this timeline is averted by Link when he travels back to retrieve the Lens of Truth and the Silver Gauntlets. This creates a second timeline, one in which Ganon is defeated.
Which would be one timeline. If anything Ganon conquers Hyrule and then seven years later the "hero" mysteriously returns (we cough this up to time travel but Nintendo easily could've said he was honing his skills in the mountains or went into hibernation or whatever excuse they wanted) and defeats him. That's a single timeline. There's never any evidence that this timeline splits. In the end you defeat Ganon, end of story, resulting in one timeline. There's never a hint of that you're in a parallel dimension in which you actually returned. If there's a parallel dimension for that then, by their logic, there's infinite timelines from having Ganon die at birth to Link slipping out the door when you leave the house and die.
However, Zelda sends Link back through time to (presumably) when his quest began. This changes the second timeline, into one where Ganon is defeated and the hero's bloodline no longer exists.
...Why couldn't Link have, armed with the knowledge of Ganon's impending takeover, warned Hyrule or saved the Princess? Hell, with access to time travel, why didn't Zelda just send Link back in time to where Ganon was vulnerable (like at his birth or something) and kill him there? It seems more logical than expecting a small child to travel through god-knows-what to retrieve these "artifacts" to help an older version of himself (by "older" I mean pretty much in the middle of puberty) to fight a godlike being with unimaginable power. OH BUT HE'S THE HERO OF TIME SO HE HAS TO WIN. When you mess with time travel you mess with gaping logic holes.
This also creates the third timeline, one in which Link warns Zelda and the King, Zelda sends Link off with the Ocarina of Time to protect it from Ganondorf, they attempt to execute Ganondorf but fail, and instead seal him in the Twilight Realm.
Which is exactly what I said before and what seems like the most logical option outside of sending Link to Ganon's inception and destroying him there. If you wanted to continue with their asspulling and say Zelda's power only permits him to send him back this far, then it seems the most logical. I mean they couldn't have anticipated that Ganon just wouldn't die at excecution and exiling him to the Twilight Realm seemed like a plausible solution. And then Twilight Princess would be rather tightly sealed and not full of a large amount of plot holes, mainly because it didn't involve bullshit like time travel.
Any other timeline that exists, like for example in MM or OoA, all ultimately lead to the same end: the Moon (or Veran) extinguishes all life. ALL of those timelines are thus irrelevant, as there CAN'T be more games in them, because there's NO MORE STORY to tell.
Yet Link does a Groundhog Day and continually repeats three days to stop the moon. This again to lead to infinite timelines pretty much. EDIT: And if Nintendo were to continue with this "timeline", they'd probably go with the canonical ending where the moon is stopped. Although with this timeline it basically shows Nintendo will say a big ol' "fuck you" to logical plot development and expansion and just use non canonical plot threads. I'm betting their next game takes place in an alternate dimension where Link never learned how to swim in Wind Waker and died when he slipped out of the boat before the first temple. Then evil took over and the world split into smaller worlds with their own types of gravity and environment. A new Hero of Time then arises (probably Link from Ocarina of Time when Zelda decides to shoot him into the future here but use her Magical Fairy Dust to make sure he doesn't age) and has to complete a series of platforming challenges to stop Ganondorf from becoming larger and more powerful. We'll call it Super Zelda Galaxy.
Time travel is an ultimate form of terrible deus ex machina. If anything it shows poor writing and development on their part. There's times when it works when it's well written and thoroughly explained (Back to the Future, Star Trek when it's not that bullshit Enterprise pulled), but basically just using it to create as many parallel universes as you want is just an incredibly shitty way to string together the unrelated plots of several games in a single series. This timeline isn't "deep" or "well thought out".
