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I know what you mean. Some people say it's Aganaham (or however you spell it). It IS him, in a way, but he's not the MAIN boss in A Link to the Past... -_-6

Oh yeah, and some people say that it's Ganondorf, when it's really ganon. There IS a difference...

Ganondorf is a gerudo, not a hyrulian. but that's all right, we all make mistakes.
3nodding 3nodding

After he was imprizoned in Ocarina, the legend actually begins. Every 300 years, the seal between the worlds (sacred realm/dark world and hyrule/light world) become weak enough to break. The only way to break the seal is by pulling out the master sword with Link. A new Link is born every 300 years; a reincarnation, like a pheonix except that insted of fire powers you get a pointy hat. The evil wizard Afgammon utilized the weakness to contact Gannon/Gannondorf and in return for power, to collect the sages, destroy the seal, and release him from his dark prision. This is my favoritest Zelda game.

People who don't realize that are stupid. They even mention that it's Ganon in the game.
@takocos: If this was your favorite Zelda game, wouldn't you know that the wizard's came is Agahnim?

We all know that Ganondorf became Ganon. It says so in lots of the games. And as for Agahnim, when you beat him in Ganon's Tower, Ganon rises out of his corpse, turns into a bat, and flies away.

I've beaten the games a lot, too. And if you read the text, one of the girls (I think from the Swamp Palace) says that Ganondorf did become Ganon, playing on the fact from Ocarina of Time, Ganondorf became Ganon (actually it was done in A Link to the Past first, released '91 compared to Ocarina's '98 ). From a Text Dump:
Link, because of you, I can escape from the clutches of the evil monsters. Thank you!...The Triforce will grant the wishes of whoever touches it, as long as that person lives...That is why it was hidden in the Golden Land. Only a select few knew of its location, but at some point that knowledge was lost...The person who rediscovered the Golden Land was Ganondorf the evil thief. Luckily, he couldn't figure out how to return to the Light World......Well, remember that you have magical powers, which only The Hero can make the most of! There are some other magical warping points like the one you saw on Death Mountain. By using them you can go between the two worlds and find the evils hidden in the Dark World. You are the only one who can destroy Ganondorf, the thief-no, Ganon, the evil King Of Darkness!
As for Link, it never says that he is descended from Zelda, but definitely from Link from Ocarina of Time. It states that he was the last of a bloodline who defended the Royal Family.
The Sage Girls are where I'm stumped. Ocarina of Time doesn't connect completely with A Link to the Past, mainly because of the races. Why didn't we see Gerudos, Shiekahs, Gorons, Kokiris and the Ocarina Zora sages? Because in Ocarina of Time they decided to play around with different races and that's where they came from. And in the beginning, it mentions an imprisoning war, but not THE Imprisioning War that most Zelda fans associate with Ocarina of Time.