Ganon's 2nd appearance was as the final boss of The Legend of Zelda: A Link to the Past. He is revealed as the new holder of the Triforce who was sealed away by the Sages into the Dark World. As he manages to break back into the Light World, Link dives into the heart of Dark Word to finally end his reign.
It took me a LONG time to beat A Link to the Past, so facing Ganon was really rewarding. A superb fight as well, except instead of going invisible he now throws a boomerang staff.
In the direct sequels Oracle of Seasons, and Oracle of Ages, the game's endings link up in a special plot where Ganon is revived. But not fully, as he becomes a raging and mindless beast. My brother had those games and not me, but he enjoyed getting to it.
This incarnation of Ganon's last form would be in Link's Awakening as a Shadow Boss. Since the game is really a dream in Link's mind, he's nothing more than a nightmare. A fight not hard to conquer either.