I believe OoT is first in the timeline because Eiji Aunoma said so.
Second is TP because the worlds are still relatively the same. Not a lot of difference from continental drift. Also, I think OoT would've had a map that was even more similar had the N64 as much power as the Cube.
I suppose you noticed I didn't say Majora's Mask despite the fact that it's clearly a direct sequel. Well I don't think that ever happened. Look at it. All the characters in MM are exact duplicates of characters in OoT. In a few cases, they even have the same name. You know how they say you see your life flash back before your eyes when you die? Well, I think Link Died at the start of MM when he fell. He was in a magic forest at the time when he died, and what do you eat in a magic forest? Magic mushrooms. I figure they made him go a little loopy, and his flashback of his life happened while he was high.
Third, I think Minish Cap because it's referenced to in Wind Waker. Sometime in the starting prophecy scene, it says a few things about the original Hero, and then it says something along the lines of 'An evil Wind blew'. I figure this is Minish Cap, Vaati being the Evil Wind.
Next I figure is Link To the Past, once again figuring by geography. It's not exactly the same, so perhaps a decent gap between this one, maybe even a hundred years.
After that, I think Four Swords followed by FS Adventures. They have to be directly related because in the second one, you automatically know how the Four Sword works, and Zelda doesn't have to explain it.
Then Wind Waker and PH, as another direct sequel after Hyrule has sank, (for which I have not yet figured a reason) and then he loses his way and ends up stranded on an island when his boat crashes. Thusly, Link's Awakening.
That's as far as I ever figured, I dunno where the Oracle Series or the first one goes, and I've also decided that Wand of Gamelon and Faces of Evil never happened, as they were blasphemy, and the second one barely made it into the timeline, but I never figured out how it got into the timeline either. Also, I never played Zelda's Adventure, so I dunno for that one. I might sometime. Maybe. Until that day which may not be ever, I shall leave it out as well. Though I will be thinking about those other ones, and may post again later on the subject if I come up with anything.