Fans of The Legend of Zelda are no strangers to dark themes, even with almost every game being rated E for Everyone, which just goes to show that a game doesn't have to have a Mature rating to be considered dark. Kidnapping, mass oppression, mass destruction, and even murder are all things that have gone on in the many different Zelda titles.
These things are usually at the hand of the main antagonist of the particular game, who either seeks to claim Hyrule for themselves or destroy it. That main antagonist often turns out to be some sort of iteration of Ganon, though he's not the only dark character within the series.
8 Beedle
Beedle appears in several different games, first debuting in The Wind Waker. The most recent versions of Beedle from Breath of the Wild and Tears of the Kingdom depict him as an insect-obsessed Hylian that works as a traveling salesman. When players talk to him, he's cheerful and peppy, offering interesting facts about insects that he buys from the hero, but his friendliness wavers if Link refuses to trade him a beetle from his inventory.
He protests, claiming that his offer was a good one, and insisting that the beetle wants to be with him. When he believes that Link has left, he begins talking to himself about how he'll steal the rare beetle from the hero and swap it for a regular one, believing that Link won't know the difference, but he decides to hire someone else to do it, in order to avoid getting his hands dirty.
7 Happy Mask Salesmen
A mysterious and ominous character, the Happy Mask Salesman appears in several games. He first appears in Ocarina of Time as the owner of the Happy Mask Shop, where he recruits Link to work as a happiness salesman, tasking him with finding buyers for each of the shop's four masks. He is generally very cheerful when speaking to Link, but when the player tries to return to the shop without making a sale, his true colors show.
His demeanor darkens and he threatens Link. He returns in Majora's Mask and teaches Link the Song of Healing at the end of the Third Day, allowing him to transform himself back into a Hylian by turning the Deku Butler's Son's spirit into a mask. However, upon learning that Link has failed his task, he grabs Link and shakes him angrily, revealing that he still has a mean streak that he hides.
6 Master Kohga
Master Kohga and the Yiga Clan are a new set of adversaries to the Zelda series, introduced in Breath of the Wild. Though Master Kohga is lazy and probably not the brightest banana in the bunch, he and his followers present a real problem for Link as they want to kill him. Some of Master Kohga's most evil deeds are in the spinoff game, Hyrule Warriors: Age of Calamity.
Set before the Second Great Calamity, Master Kohga impersonates Urbosa and sets the Gerudo against Princess Zelda and her group. He tries to attack Zelda, but before he can, the real Urbosa shows up to stop him. This act alone is particularly dark considering how close Zelda and Urbosa were, so thinking that the Gerudo Chief was her enemy was a deeply personal betrayal.
5 Vaati
Vaati isn't as big of a villain as Ganon in the series, but it's still undeniable that he is a dark character. Appearing as an antagonist is Four Swords Adventures and The Minish Cap he's an evil mage that was sealed away by the Four Swords and was unleashed when the seal on the sword was broken.
Aside from spreading his darkness across Hyrule and trying to kill Link, he has the Shrine Maidens kidnapped and sealed into crystals, while he takes Princess Zelda back to his palace in the sky and tries to force her to become his bride. In The Minish Cap, he turns Princess Zelda into stone and gradually steals the Light Force from her to power himself up.
4 Majora's Mask
Majora's Mask is an object inhabited by an evil spirit, known as Majora. It was used as part of various rituals by an ancient tribe until it became so dastardly that they were forced to confine it in order to protect the world. Little is known about its history, but once it is able to take possession of Skull Kid, it is shown to have enough strength to turn adults into children, and even pull the Moon down from the sky.
In the final battle of the game, Link must fight Majora's Mask through three separate stages. The first stage is called Majora's Mask, and it is a form where the mask itself has sprouted tentacles. The second form is called Majora's Incarnation, where its tentacles give way to arms, legs, and a small head with a single eye peeking over the top of the mask. The final form is known as Majora's Wrath. It is a full-on humanoid form armed with tentacles that come from its hands.
3 Zant
Zant is the main antagonist of Twilight Princess. An inhabitant of the Twilight Realm, Zant usurps the throne from its rightful ruler, Midna, stealing her powers and even turning her into an imp-like creature. He goes a step further and transforms the other inhabitants of the Twilight Realm into Shadow Beasts.
He has committed several horrible things that put him in the same sphere of darkness as Ganon. These atrocities include invading Hyrule, threatening the total annihilation of all the people of Hyrule, ordering the execution of the Zora queen, Rutela and almost killing Midna.
2 Ganon
Whether he's Ganondorf, Calamity Ganon, or just plain old Ganon, most fans would agree that he is one of the darkest Zelda characters. Even back when Ganon wasn't a monster, he was up to no good. He was the leader of a group of thieves in A Link to the Past, and he corrupted the Sacred Realm. As the King of the Gerudo in Ocarina of Time, he menaces Hyrule and even his own people.
He's a power-hungry, manipulative individual that will do whatever he feels he needs to do to get what he wants. It's not a stretch to call him a megalomaniac. In Breath of the Wild, he literally takes on the form of a monster that is the amalgamation of the primal evil of Hyrule.
1 Demise
If there was a character that could be considered the ultimate evil of the Zelda games, that title would go to Demise. The original Demon King, Demise sought to take the Triforce from the Goddess Hylia but was defeated. Before his defeat, he waged a war with the people of the Surface and he and his demon horde caused widespread destruction, death, and general misfortune all across the land.
He gets resurrected in Skyward Sword by absorbing the soul of Princess Zelda and when he is ultimately defeated by Link, he places a curse on himself, and the descendants of the Goddess and the Hero, saying that an incarnation of his evil will be reborn for eternity and always seek to claim the world as his own. The curse also makes those born with the blood of the Hero and the Goddess be caught in that same cycle of rebirth.