Spoilers ahead!
Zelda timelining is more an art than a science,. There is a continuity... of a sorts... but it is vague and almost contradictory.
It is not helped by flat-out contradictions made by the game makers. LTTP clearly states it is a prequel to the original LoZ, and the designers said so at the time. Biut since, some designers have made out it was not.
Meanwhile, the 'split timeline' theory long advanced by many fans was given unexpected credence by one of the game makers during Wind Waker's cycle who spoke about Ocarina of Time having two endings and WW being a sequel to one of them. Eeek!
Here are some generally useful guidelines
1. Don't get too worried about Ganondorf dying and coming back; he's a weird supernatural creatue and drama states that these things come back after seemingly being 'killed'
2. Hyrule's geography is almost entirely random and it is not worth trying to build anything out of that- though there are some interesting parallels between Twilight Princess and ALTTP in that area
3. We can make some assumptions/deductions- some stronger than others biut none totally unreasonable- that help us put this into context
Here are those assumptions/deductions:
A. The Minish Cap, has elements that suggest they are before the existence of the Master Sword, the Triforce and the concept of the recurring Link hero. The last of those three- the green-capped Link who will be echoed throughout the Ages- may come into being at the end of MC. So it is not objectionable to say that this is some kind of pre-prequel, looking at some origins (the direct relation between the Golden Force and the Triforce of other games is unclear; the writer spoke of the Golden Force being an ancient, and maybe related, legend but a separate thing. Judging by appearance, many fans took it for granted that the Golden Force is the basis of one third of the Triforce)
The Four Swords games, though written earlier, clearly come after TMC (beginning as it does with the bad guy released from the imprisonment that occurs at the end of TMC) but presumably MUCH later as Ganon turns up there as well.
B. Ocarina of Time is the easiest to out into continuity, both for story elements and because no game designers have ever contradicted or confused the issue. The Master Sword already exists (possibly foretold by Minish Cap), inside the Temple of Time, likewise the Triforce is solidly in place. Link is already green-capped but the concept of the recurring Link has not yet become well known, though it may already be happening- Link is the mysterious Human boy in a village of faries, after all, already out of place. Ganon(dorf) is the Thief-King of the Gerudos, and during the course of the game becomes empowered by the Triifoce, becomes the bg demony thing we tend to generally associate him with being, and gets sealed off in the Sacred Realm at the end by the Sages (re-named to Sages rather than 'wise men' because... well, some are female) jist as the rest of continuity has established.
Majora's Mask directly follows on from OOT- easy. However, Link seems to have lost his triforce; Wind Waker makes an obscure comment suggesting it got shattered at this time.
C. Wind Waker happens centuries (or 'a century'? This issue has become complicated by designers) after the Adult ending of OoT, (or just THE ennding if you think there is just one) where the land was battered and broken and ravaged, but Ganon was locked away in the Sacred Realm. Hyrule has been flooded
Spoiler:
to prevent Ganon escaping as his seal weakens
, the existence of Link (but not a recurring Link) is well known; at the end, the whole lot is sealed up again.
The Phantom Hourglass will sequel this but likely won't mess around with continuity elements, though we will see
D. Twilight Princess is an arse to quantify. It's post Ocarina, certainly. The geography, as I say, has certain resemblances with ALTTP. The Master Sword is in the old grounds of the Temple of Time, now broken down and abandoned (but still connected by Time to its old self), and the area around the Master Sword is becoming analagous to the Grove in which you find it in in ALTTP. The original Link is well known of, new Link has a Triforce, it all fits between those two stools. So that bit's easy.
The tricky bit is, although the evil Ganondorf is well known of, there is no reference to him being banished to the Sacred Realm (though the Sacred Realm is referred to heavily relating to the Twili, and the creation of the Twilight Realm), the Sages exist but seemed surprised he was in possesion of a Triforce, it;'s hard o make out if it is pre-flood or pos-lfood or in the same continuity as the flood... who the Twili were is a mystery (could they have been the Gerudo? Soe of Midna's speeches could be interpreted to make out that Ganon was once their King, but nothing definite- regardless, the Gerudo have stopped existing)... the Zora and Gorons are still there, but the Kokiri seem to have buggered off... all a mystery, that one. Some speculate this comes after the child ending of OoT... but it's hard to be sure of anything
E. A Link to the Past DEFINITELY comes after all of those. Ganon has turned the Sacred Realm into a land of evil, and the descendants of the Sages are those he kidnaps as the seal weakens and he threatens to escape, before new Link stops him, possibly the final time the Master Sword is used (as I say, taken from a grove not unlike the area in TP was becoming). How Hyrule became unflooded, or if it became refounded, and how Ganon weaklened the seal when flooded... none of this is known (or was even relevant when the game was made).
Link's Awakening comes after this directly, and I THINK the Oracle games do as well, but I've never played them and have no real clue.
F. Plenty to be unsure about, so now the final puzzle is the original two games. Link's Adventure, of course, comes after Legend of Zelda. But is LoZ before or after ALTTP, and if before, where before? Hyrule is a wasteland, though that might be artistic licrense considering how old the game is. Only one third of the Triforce is known of, and is shattered; the second third is focussed on in Adventure of Link. Much logic say ALTTP preceeds these games- not least the back of the LTTP box- but then you wonder when the triforce shattered, certainly when Wind Waker suggests it happened back at the time of Majora's Mask... but it's back by Twilight Princess...
...
Ah, it's a mess. make of it what you will.
The split timeline theory says that one Hyrule dates from the one Ganon destroyed in OoT, that Link was an adult in, and got sent home from at the end (becoming a legend). The other is the timeline he returned to, where (presumably) Ganon never came to full power and Link lived out his normal life.
Like it or lump it, it is gaining credence. But SO little is certain about any of this, and they are clearly winging it at Nintendo, just come up with whatever you like