Ganon is the main villain of The Legend of Zelda series, but he hasn't been the foe in every entry in the franchise. In fact, there are several times when Ganon hasn't appeared and had his spot as the final boss filled by other villains.
The series has a confusing timeline, which splits at the ending of Ocarina of Time. The battle at the end of Ocarina of Time created three timelines: one where Link died, one where Ganon was defeated, and one where Link was sent to the past and Ganon returned. Ganon (like Link and Zelda) is reincarnated across the centuries, which means he has appeared in different forms throughout the series, culminating in the monstrous Calamity Ganon in Breath of the Wild.
There are some Zelda games that are set in timelines where Ganon is defeated, or at points in time where he doesn't exist. These games feature different foes for Link and Princess Zelda to fight in climactic boss battles.
Zelda 2: The Adventure Of Link - Dark Link
Ganon is killed by Link at the end of the original Legend of Zelda game. In the sequel, his servants are attempting to bring him back to life with Link's blood. Ganon appears on the Game Over screen, but cannot be fought in battle. The final foe in Zelda 2 is Dark Link, offering Link a mirror match before he can awaken Princess Zelda.
The Legend Of Zelda: Link's Awakening - Nightmare
Link's Awakening takes place inside of Link's dreams as he's floating out in the ocean. The final foe he faces is Nightmare, which is the literal manifestation of Link's nightmares. Nightmare does take on Ganon's form at one point during the battle, but this is only an illusion. It bears mentioning that Ganon is briefly revived at the end of the second run in either Oracle of Ages/Seasons, but this is a mindless form that only appears at the very end of the game, as the villain in those titles is actually Twinrova.
The Legend of Zelda: Majora's Mask - Majora
Majora's Mask is set in the timeline where Link killed Ganondorf at the end of Ocarina of Time. As such, the villain of Majora's Mask is an evil spirit named Majora, who possesses the titular mask. Majora's Mask is controlling Skull Kid throughout the events of the game. Young Link must challenge the terrifying aspects of Majora within the moon, in order to save Termina.
Legend Of Four Swords - Vaati
Vaati is a wind mage from ancient times, who was sealed away by the power of the Four Sword. Vaati awakens in modern times and kidnaps Princess Zelda. It's up to Link to wield the Four Sword and break himself into different people, in order to defeat Vaati and save the world. He returns as a foe in Four Sword Adventures, but Ganon is the main villain in that game.
Minish Cap - Vaati
Vaati's backstory was fleshed out in The Minish Cap. He was a member of the Minish race, who turned to the dark side and transformed his master into the titular cap. Vaati uses his powers to open the Bound Chest and unleash the evil within. He turns Princess Zelda to stone, as her power is capable of stopping him. Link must restore power to the Four Sword and defeat Vaati (again).
The Legend Of Zelda: Phantom Hourglass - Bellumbeck
Phantom Hourglass is set after the events of Wind Waker, where Link killed Ganondorf at the end of the game. The villain in this game is Bellum, an evil spirit who cursed the Temple of the Ocean King. Link must create a blade called the Phantom Sword to be able to defeat Bellum. At the end of the game, Bellum possesses Linebeck, becoming the monstrous Bellumbeck. Link is able to cast Bellum out of Linebeck's body, destroying the phantom once and for all.
The Legend Of Zelda: Spirit Tracks - Malladus
Spirit Tracks is set in the same timeline as Phantom Hourglass, so there's no Ganon here either. The villain is a demon king named Malladus, who was once sealed away beneath the ground, creating the Spirit Tracks in the process. Followers of Malladus manage to free him, with the aim of using Princess Zelda's body as a spirit vessel. Link (and the ghost of Zelda) must work together to prevent the return of Malladus. In the end, Malladus is forced to inhabit the body of one of his followers, allowing Link and Zelda the chance to defeat his demonic form.
Tri Force Heroes - The Lady
Tri Force Heroes was a much more light-hearted game than the other Zelda titles. The villain of this game was The Lady, who put a curse on Princess Styla, forcing her to wear the Cursed Tights. It's up to Link (and two other Links) to track down three items that will allow them to break the curse. The final item is The Lady's Parasol, which is currently owned by The Lady, so the Links must find her in the Sky Temple and defeat her.
A Link Between Worlds - Yuga-Ganon
Yuga is a sorcerer with the power to turn people into portraits. At the end of A Link Between Worlds, Yuga revives Ganon and fuses with him, becoming Yuga-Ganon in the process. This one almost didn't make the list, but it's clear that Yuga is the main antagonist and Ganon is just a source of power, so he just made the cut.
The Legend Of Zelda: Skyward Sword - Demise
As Skyword Sword is the earliest point on The Legend of Zelda timeline, it predates the existence of Ganon. The villain in this game is a demonic being called Demise, who was sealed away centuries earlier, but is able to manifest as The Imprisoned. Demise is brought back to life by Ghirahim but was defeated by Link. Demise utters a final curse before he perishes, which seems to be the source of the endless cycle of Ganon/Link/Zelda rebirth in The Legend of Zelda series.
