The characters on Supernatural often oscillate between light and dark, much to the benefit of the plot and the delight of fans. Thus some of the most popular characters on the show are villains, of which there are many.
Many villains switch allegiances over the show's fifteen seasons. Some form temporary truces; some take a while before revealing their true colors, but no matter what the reason, most of the major villains in the show have at least one little moment of being a hero.
Alternate Michael Defeating Lucifer
Michael was the absolute worst when he was first introduced in the Kripke-era of Supernatural. He was the ultimate good-little soldier character who never knew why he was doing anything, but simply followed orders he was given.
The alternate reality Michael was somehow worse. Just a more jacked-up version than the Winchester world version, alternate Michael was far more successful in his evil plots than original Michael was in bringing the Apocolypse. However, unlike the original Michael, alternate Michael managed to get a proper face off against Lucifer and defeated him in a terrible fight. This was the only good thing he did before taking Dean's body in an attempt to take over the world.
Cain Saving His Brother
Cain is one of the most important minor characters of the final half of Supernatural's fifteen-year run as he is the one who passes on the Mark of Cain to Dean, kickstarting a domino effect of events.
Cain turned out to be not too much better than most demon villains, but after being controlled by the Mark for that long, it's understandable. Cain killed his brother Abel, but only because Abel was being seduced by Lucifer, and Cain made a deal to kill his brother and send him to heaven, taking his place in hell and as a Knight of Hell.
Lucifer Resurrecting Sam
Nobody could have predicted the longevity of Lucifer as a character in the show when he debuted in the Kripke-era; he was one of the most prominent returning characters and played a vital role in a slew of storylines.
He was nearly always the villain, though, and while he was forced to team up with the Winchesters on one or two occasions, he did not perform many heroic acts. Arguably the best thing he ever did, though, was bring Sam back from the dead after vampires in the alternate world mauled him. Of course, Lucifer did this for his own selfish goal of getting to Jack, but he still did it; without him, Sam would not have made it through the rest of the show, which is ironic since he was nearly the cause of his death in season five.
Ruby Saving Sam & Dean
One of the most famous and important characters in all of Supernatural is Ruby, who at first presents herself as simply a demon who hates demons and wants to help Sam and Dean before revealing her true colors.
Nevertheless, she hid her true intentions well, and in doing this, she performed a decent amount of heroics, perhaps most notably on her debut when she and her iconic knife saved Sam and Dean from the Seven Deadly Sins after hell got busted open.
Metatron Sacrificing Himself
This will not be the last sacrifice to pop up here. The first villain to sacrifice themselves in a heroic act is Metatron.
The villain who manipulated Castiel, cast the angels from heaven, and attempted to play God, even killing Dean Winchester, eventually became an ally to team free will, particularly when Amara popped up. Metatron ended up confronting Amara, allowing the other heroes to escape before she killed him mercilessly.
God Resurrecting The Heroes
God is the absolute worst in Supernatural. Plain and simple, Chuck is a spoiled brat, and definitely not the individual anyone would want to be the creator of everything and the omnipotent one in the Universe.
It takes a while for Chuck to reveal how much of a villain he truly is, but in terms of heroics, it does not go much further than the number of times he admitted to playing a part in Sam's, Dean's, Castiel's, and Bobby's survivals and resurrection. This definitely throws a wrench in the meaning of life for the heroes, but still, keeping them alive is just about the best thing God manages to pull off in the show.
Gadreel Joining Castiel & Sacrificing Himself
Gadreel, who originally portrayed himself as the revered angel Ezekiel, was a fascinating angel. He was despised by his kind and seemed to genuinely always want to do good, but never quite understood what that meant. He eventually became allies with Metatron.
Eventually, the secondary-villain realizes the damage Metatron has and will cause to the angel kind and decides to side with Castiel, a move that saw him slashed up by Dean and ended up in an angel jail with Castiel. In order to stop Metatron and save heaven, Gadreel destroyed the prison at the cost of his life, allowing Castiel to escape and stop Metatron.
Amara Resurrecting Mary Winchester
Amara, also known as the Darkness, was a bizarre villain as far as the Supernatural rogue's gallery goes; from her weird relationship with Dean to the vagueness of her intentions, she is not the most popular villain ever.
Then again, she is immensely powerful, with the ability to do a lot of damage, even to Chuck. Luckily thanks to Dean and the heroes, Amara and Chuck leave together to air their grievances and be a family again, prompting Amara to thank Dean in a huge way by bringing back his mother, Mary, from the dead, the thing he apparently wanted most.
Rowena Sacrificing Herself
Rowena MacLeod is a character who died multiple times throughout Supernatural but gave her final goodbye in season fifteen when she sacrifices herself to pretty much save the world.
Through the use of her powerful magic, she absorbs all the souls escaping hell after being fatally stabbed by Sam (consensually). She then descends into hell herself where she becomes the new Queen. It was a fitting end for such a phenomenal character who went from villain to anti-hero to villain to straight-up hero multiple times in her five seasons on the show.
Crowley Sacrificing Himself
As popular as Rowena was amongst the Supernatural fandom, the title of most popular Supernatural villain will always belong to her son Fergus, more commonly known as Crowley, the King of the Crossroads, the King of Hell.
Crowley is another character whose allegiances switch on a whim. He has been the main villain, a villain, an anti-hero, a hero, half of a bromance with Deanmon, and was one of the show's best-developed characters post-Kripke. His ultimate death came when he acts as the final step of a rift-sealing ritual to trap Lucifer in an alternate reality. It was his ultimate heroic act and one of many he makes over the years.