Volume II: Q & A

A Link to the Past

Agahnim is Ganons alter ego, but what is this beings past?

Observing his clothes, he appears to be a Sheikah. Look at the symbol on his robe (the artworks, not the game) and the carpet in the castles tower (the room before his): an eye with something similar to tears, almost the same symbol seen on the gossip stones and on Sheik's chest. Also in his second battle he used shadows to fool Link.
He could be a magically conjured being, like Phantom Ganon, but one may also deduce from Soul Calibur II that Agahnim used to be a person of his own, a wizard turned evil. So Ganon might have possessed him for Agahnim to be his alter ego (as he does with another puppet at the end of TP).
This explains why he fights somewhat, but not entirely, like Ganondorf. In any case, I would assume he's been Ganon's alter ego for quite a while seeing how there are statues of him on the Dark World's pyramid.
It also goes without saying, that his title of -heir- to the Seven Wise Men is merely honorific. Being their heir doesn't necessarily mean he is their descendant.

Why are the "surnames" of Ganondorf and Ganon, Dragmire and Mandrag respectively, absent from both the games and this site?

Because that is something the people who localized ALttP's manual made up.

Why are there in A Link to the Past warp tiles that allow entrance to the Dark World?

No reason is given by the game for their presence. Probably when A Link to the Past was released, they were supposed to be the entrances to the Golden Land mentioned in the booklet; one of which was used by Ganondorf to obtain the Triforce. It was also speculated that Ganon made attempts to escape his prison and thus some openings started to form (openings between the dimensions not the seal, mind it).
Some also have noted that most of the Temples in Ocarina of Time are placed near to where these tiles were (or would be). Perhaps when the Sages could heed their call to the Sacred Realm some openings were left behind; but I don't think so.
In the end, the phenomenon seems to finally have been explained by the portals Link opens in FSA.

Is it the Triforce that changes anybody who enters the Dark World to reflect what is in their hearts, or is it the Dark World itself?

Some characters claim it is the power of the Dark World or "magical air of the Golden Land", others that it is the Power of Gold, the Triforce, that changes people like that in order to grant Ganon's wish for the world (and it is something that doesn't happen in AST, Oracles and FSA). The relation between the wish and this side effect I can only try to guess. Perhaps it has something to do with evil greedy men entering the Dark World to join Ganon's army; giving them the shape of monsters will make them more dangerous, while those who are not evil may be hindered by the change (as Link was). We know for a fact that those who wandered into the Dark World could return to the Light World and their shape once Link obtained the Triforce. The only way to avoid conflicts, is to say that the Triforce, to grant Ganon's wish, made the air of the Golden Land/Dark World change people who enter it.

Why doesnt Ganon, in A Link to the Past, simply wish on the WHOLE Triforce for the Sages Seal to break or for Link to die? Isnt the Triforce omnipotent?

A: (Caution spoilers)
Even though the Triforce is omnipotent for it can grant any wish (as long as its master's wishes it strongly enough), its might can still be countered; the Master Sword can deflect its magic protecting the user from it (I don't mean deflect as play tennis, I mean that Ganon can't wish for Link to disappear as long as he has that sword) and evidently the Wise Men's Seal can do that too (notice though that Link is still changed to reflect his heart as he enters the Dark World, evidently the sword doesn't protect him from magic the Triforce doesn't cast directly upon him, but upon the world he's in. For that he needs the Moon Pearl which either protects him on his own or in conjunction with the Master Sword to repel the evil/darkness like the Sols did in TP. After all, it did work in conjunction with the Four Sword in FSA).
Casting the Seal, Rauru chants a plea to the Goddesses; supposedly that's why the Seal is strong enough, because it is empowered by them. The Master Sword also was forged by them in compliance to "the gods' oracle" (long before the Imprisoning War, as demonstrated by OoT and despite what the English manual of AlttP may say). Furthermore we can see from TWW that the sword takes its power to repel evil (and resist the Triforce) directly from the Gods.

Just how did Ganon get the whole Triforce in ALttP?

Now this ones going to be long. When ALttP was originally released, anybody playing it could easily tell it was meant to take place before LoZ and AoL. That is because of the following reasons: both in the manual and the game, was said that Ganon entered the Golden Land, obtained the Triforce that was supposedly there from the beginning of time, and from there sent an army against Hyrule; Ganon and the Triforce were then sealed in the Golden Land (now Dark World) before they could ever leave it. In the end of the game, the united Triforce was brought to Hyrule by Link, and thus it was possible for the back story of AoL to take place; that is, the King ruling with the Triforce (which could not happen before ALttP since Ganon is implied to be the first that took the Triforce and was sealed with it), his daughter cursed with eternal sleep and all princesses to follow named after her. The only plot hole was how Ganon had returned to life in LoZ, but even that seemed to be filled in with LA (the English version of LA), that stated trouble was still expected (after ALttP) from Ganons ashes. So everything made sense.
Enter OoT, mother of all confusion and plot craters. First the in-game presents discrepancies from what ALttP told us of the Imprisoning War: the Knights' role for the most part played by Link, Ganondorf who, intent on getting the Triforce, is actually succesful in conquering Hyrule, leaving the Sacred Realm with the Triforce and other details such as Link looking for the Sages and not the other way around. This obviously overlapped said previously canon material and put the rest of ALttP's manual in doubt, but a retroactive change can be accepted as long as it makes sense. Unfortunately, it also thwarts the programmers' previous attempt to explain why theres more than one Princess Zelda (as we have another Zelda that pre-dates the cursed one... and even more with later games)
What's worse, is really the way OoT makes the Imprisoning War end: not only it created great confusion by having Link sent back in time (without clearing up what was and was not undone by this), but Ganon also ended up being sealed in the Evil Realm with only the Triforce of Power! At first, I thought this could lead into Miyamotos insane statement that LoZ came before ALttP (since in LoZ Ganon has the Triforce of Power) something impossible as I explained in this answers first paragraph. Who would then be the sleeping Zelda? That of OoT? Her father never had the Triforce. A previous one? But What of the hidden Triforce of Courage? That would require for it to be hidden at a later time which doesn't make sense. Not to mention that Ganon couldnt be in Hyrule before the Seal was broken in ALttP, while he sure is in Hyrule during LoZ (see the question below for more on Miyamoto's statement).
For a while, I went with the assumption that Agahnim found the remaining Triforce parts and sent them to Ganon long before coming to Hyrule Castle. But now, as I expected, Nintendo appears to have further retroactively changed things. I'm persuaded that being sent back in time Link found himself in a new timeline where Ganondorf (still free) was unable to enter the Sacred Realm as in OoT (because Link didn't take out the Master Sword and took the Ocarina away). The events told in Twilight Princess' backstory come to pass: Ganondorf tries to conquer Hyrule but is defeated and banished in the Twilight Realm. He returns later on but Link kills him. Then in Four Swords Adventures, he is reborn, and finds another way (other than the temple of Time) to get into the Sacred Realm, now Dark World, and gets the whole Triforce (this new Ganondorf having balanced his wicked heart). Then he kills off the knights and is defeated by Link while the maidens seal him into the Four Sword. Now in ALttP that sword is in Ganon's pyramid, and certain monsters encountered in FSA Hyrule are now only in the Dark World (like the Hinox), so it's no big stretch to assume that he was sealed together with his minions in the Dark World before he could escape the sword, making everything fit; especially if we remember that the events in OoT are kept in memory by the Royal Family in both timelines, meaning the Sages and their efforts are not forgotten and both legends of Ganon's imprisonment can mix to form the background given in ALttP.

About ALttP, it appears that Shigeru Miyamoto stated it should take place after LoZ and AoL, with LA falling anywhere in-between. Isn't that a most reliable canon source?

Apparently yes, he did state that, but I'm not giving that interview much importance for the following reasons: first as said above, that when ALttP was released it was obvious even advertised that it took place before LoZ and AoL and, and in Japan too: back of the Japanese box "This time, the stage is set very long before the time when Link accomplished a feat, the epoch when Hyrule was still one kingdom", when Hyrule was one kingdom is said also of the time when AoL's backstory took place. And second, in all honesty, the other way around would make no sense at all. But there's more: contrary to popular belief, the stories of the Zelda series were not entirely (nor probably for the most part) written by Miyamoto, the one that worked them into a game (one of the best of all times may I add).
So, unlike what goes for the unequalled gameplay and feeling of exploring a fantastic world that he put into it, we owe the most of Zelda's story to script writers Takashi Tezuka and Kensuke Tanabe (for the first two and second two games respectively).
Besides, it doesn't look like Miyamoto takes the whole matter very seriously; can you imagine George Lucas making a new Star Wars movie and then state it can fall anywhere in the series?

In pratical terms, the new races of OoT were not in the previous games because they had not been conceptualized yet. But are there explanations of this absence in terms of storyline?

A: (spoilers for Oracles and TWW)
The Gorons were probably tired of the conflicts Hyrule seemed so often to face, and went elsewhere: in Holodrum and back to Labrynna. Besides Death Mountain itself became a hostile place after Ganon built his tower on the Dark Worlds own, and in the new timeline the Great Sea was a very dangerous place for Gorons.
Similarly, the the Sea Zoras likely returned to Labrynna as seen in Oracle of Ages, abandoning their outpost in Hyrule for River Zoras to take. In the other timeline they become Rito but that will be detailed elsewhere.
The same seems to apply to Deku Scrubs. Those seen in FSA were either trapped in the Dark Mirror from ages past or cursed people.
I'm not sure what happened to the Kokiri, I suppose they either returned to being Koroks (as in the other timeline) and still hide deeper in the woods (as Ordon village seems to have been built over that of the Kokiri) or now resemble/became normal people (I suspect ALttP's twin lumberjacks, "kikori" in Japanese, and the grumpy thief who has the same posture as Mido, which may be a hint).
The Sheikah were dying out already in OoT and TP because of the fierce wars previous to those games; and the Hylians, as said, supposedly mingled with other human races, losing their affinity to magic (and making their ears less pointed).
The case of the Gerudo people is far more complex, and will be elaborated upon in a question of their own among those for Ocarina of Time.

Link's Awakening

How come Koholint seems to be made with parts of other games?

A: (Caution spoilers)
If we factor the Wind Fish as being an omniscient creature, he could easily have taken inspiration for his dreams from different worlds and times (thus explaining the presence of other Nintendo characters).

Where would Koholint be in relation to Hyrule?

According to the Japanese manual, it's an island in the south. I guess that could be figured out by the palm trees.

In the end of Link's Awakening, what will happen to the hero?

A:(caution spoilers)
After Koholint vanishes, Link is stranded at sea with nothing but a piece of wood from his ship to sit upon. The unofficial manga suggests that the Wind Fish flies in the direction of land, indicating Link what direction to paddle to. But in any case, we do see lots of seagulls in the ending. These birds typically dont stay too far away from coasts, so this could indicate that land is pretty near. It is however also possible that they were whisked into the dream island too.