The Winchesters has brought some original characters from Supernatural back, but the villains have been largely unique to the new storyline. However, the new prequel also has a complex cast of villains that resembles the original.
There were dozens of villains throughout the 15 seasons of Supernatural. While many of them were purely evil with no redeemable qualities, there were also some complex villains who weren't wholly evil or had a reasonable explanation for their bad ways.
10 Rowena
Rowena has her ups and downs throughout the series. Though she begins as a clear villain, she ends up helping the brothers and eventually ends up making one of the bravest sacrifices to save the world. Even after learning she's become the Queen of Hell, she's still not portrayed as a villain in the end.
Rowena is considered one of the best villains according to fans. She ends up being a good person that redeems herself. However, much of her personality and backstory have to do with her taking care of her own interests. While this is understandable given her unique circumstances, it makes her one of the least sympathetic villains.
9 Crowley
Though he was a demon that did some ruthless things, Crowley was a villain that deserved to win in the end. He did some things to thwart the Winchesters, but he also became a valuable ally and eventually sacrificed himself to help take down Lucifer.
Crowley had a rough childhood and sad adulthood that led to him selling his soul to a crossroads demon, making his background story a sympathetic one. Though his demonic nature made him less than wholesome, he was respectfully trying to create order in Hell.
8 Death
Death was one of the Four Horsemen of the Apocalypse that was controlled by Lucifer to try to end the world. Though he is the main Reaper himself, Death is actually there to create a balance between the living and the dead.
He was only bad in the sense that he was helping to end the world, but it was due to him being under a spell. Therefore, though Death himself can't be considered wholly good, he did little wrong but do his job. This aspect is also what makes Billie only a low-key villain when she takes Death's place as leader of the reapers.
7 Lucifer
Lucifer is the embodiment of evil in this series. However, his story is the traditional archangel story retold time and time again, making him sympathetic in the sense he was dismissed by his own father, which made him evil.
Lucifer is one of those villains that is sympathetic because his nature is what causes his terrible actions and is something so ingrained in him, it's unavoidable he'll continue to do evil deeds. While Lucifer has some absurd weaknesses, his power of him being the father of evil and an archangel makes his villainous behavior understandable (even if it's inexcusable in the end).
6 Amara
Amara is the Darkness itself and, in other words, the balance of evil vs. good. She and God's (or Chuck's) creation caused a balance in the universe that was essential for creating the Earth and all of the power in the galaxy.
She almost destroyed the world and chose her brother over the stability of their universe, making her a controversial character. However, she's another character that cannot control the nature of her powers and existence, making her sympathetic in the sense she only did what she was literally created for.
5 Meg
Meg is one of the many villains that goes from extremely bad to somewhat helpful. Initially, Meg is a villain that helps Azazel and later works with Lucifer. However, she later ends up helping Sam and Dean to fight Crowley when he seeks to use the angel tablet.
Meg becomes one of the most sympathetic villains when she ends up taking care of a distressed Castiel and eventually falls in love with him. Her love for Castiel, and her hatred of Crowley, make her help the Winchesters and sacrifice herself, so they can escape the demon. Her change of heart and admirable sacrifice makes her one of the most respectable villains in the series.
4 Adam
Adam Milligan, the Winchester's half-brother, doesn't become a villain until the final season. After spending a decade in Hell, he allies with Michael because the archangel helps bring him out of the cage and back into the real world, though Michael does this by taking Adam's body as a vessel.
His return allows his brother to make amends for abandoning him, and he is content with their apology by the time Michael is destroyed, killing Adam along with him. Adam isn't necessarily a villain per se, but one that allies with one. He's a sympathetic character because, despite his questionable decision, he was abandoned and left to survive Hell for many years.
3 Metatron
Metatron is one of the most disliked villains in the entire series. He started off as the Scribe of God but turned into a villain when he is forgotten by God. He becomes a huge obstacle for the Winchesters when he incites and leads an angel rebellion that threatens the whole world.
Despite that Metatron tries to take over the world, making him one of the vilest villains, he is sympathetic because he sees the greatness in humanity that even the Creator himself can't. He proves to be a more complex character when he pleads with Chuck to see what amazing humans he's created.
2 Amy
Amy Pond is a monster Sam met in childhood and later becomes a case they investigate when she starts killing people to take their brains. However, when it's revealed that she normally only eats the dead and was only killing to heal her sick son, she proves to be a very sympathetic villain.
There's certainly no excuse for killing people, but it was admirable and understandable that Amy was doing so to protect her child. She had been raised by a killer mother and had vowed to never kill people, making her even more sympathetic because she had no intentions of killing until she was forced to choose between her evil side and her child's life.
1 Jack
Jack Kline is one of the most controversial characters in the series. Some fans love him and some can't stand his inclusion. Either way, viewers are conflicted about whether to call him a villain or not, especially since he takes God's place in the finale.
Whether he can be considered a villain or not, it was undoubtedly wrong that he killed Mary Winchester and then tried to hide it from her sons. However, Jack has a complicated story and struggles with his powers from the time he's born. His complex story makes him sympathetic even if he does some heinous deeds in a moment of uncontrollable anger.