Definitely Naruto himself (as the gender - bended version). Since the whole concept often revolves around him changing genders, he's at the center of most of these fanfictions. Another popular character would be Sasuke. His relationship with a gender - bended Naruto always makes for an interesting dynamic.
Probably Female Thor. She brings a new and exciting take on the character. Her story can be different from the male Thor's, like how she might handle her relationships with other Asgardians or mortals. Another popular one could be Male Black Widow. People are often interested in seeing how a male version of this complex and deadly assassin would operate. And also Female Iron Man. The idea of a woman in the role of Tony Stark, with her own unique style and approach to technology and heroism, is really appealing.
Natsu is quite popular. Since he's one of the main characters, seeing him as a female brings a whole new dimension to his relationships and his fiery personality. People like to imagine how his interactions with Happy and the rest of the guild would be different.
Harry himself is also a common character for gender - bending. As the main character, changing his gender can completely shift the narrative. It allows for new interpretations of his hero's journey and how he deals with the challenges of the wizarding world as a female. Fans are interested in seeing how a female Harry would handle things like the Triwizard Tournament or facing Voldemort.
Definitely Harry. Since he is the main character, a gender - bent version of him can lead to many different plot twists. Fans are often interested in seeing how a female Harry would interact with the other characters and change the course of the story.
Obviously, Naruto is the central character as the one whose gender is changed. Sasuke is often a part of the harem, his brooding nature adding an interesting dynamic. Sakura might also be included, but in a different role, perhaps as a friend or a rival to the female Naruto. Kakashi could also show up, being a mentor figure who has to deal with this new situation.
Obviously, the gender - bent Batman is a popular character in these fanfics. Writers often like to explore how this new version of the Dark Knight would interact with the existing Gotham City characters.
It has a decent level of popularity. There are many fans who enjoy this genre as it offers a unique take on familiar stories. In some fandoms, it has a significant following, especially those with large and active fan communities.
One idea could be Naruto being turned into a girl and having to deal with different social expectations in the ninja world. For example, she might face more restrictions in combat training at first because of the traditional gender roles. Another plot could involve the reactions of his friends like Sasuke and Sakura. Sasuke might be more protective or have a different dynamic with a female Naruto.
One popular pairing could be Sakura (as a male) with Naruto. Their friendship already has a strong foundation in the original story, and with Sakura's gender change, it could develop into a romantic relationship. Another might be Sakura (male) and Sasuke. Their rivalry and underlying connection could take on a different form as a same - sex relationship in the gender - bender concept.
Well, Naruto is no doubt a top choice. He has a huge fan base already, and in Dark Slayer style fanfiction, fans are interested in seeing how he would handle the new and dangerous dark powers. Sasuke is another one. He has always been on the edge between light and dark, so it's natural for him to be a central figure in these stories. Then there's Orochimaru. His obsession with power and his dark experiments make him a very fitting character for Naruto Dark Slayer style fanfiction. He can be either the main villain or a source of the dark powers that others are after.