Yes, there are many. You can find them on popular fanfiction websites like Archive of Our Own. Some might focus on their relationship development, from how they first met to falling in love. There are also ones that explore their adventures together within the Supernatural universe.
One common theme is love and romance. Since their relationship has potential in the show, fanfictions often explore how they fall in love. Another theme is adventure. They might go on hunts together and face various supernatural creatures, which is in line with the Supernatural series itself.
Writing fanfic involving sexual content is generally not appropriate as it goes against ethical and moral norms in many cases. It can also be disrespectful to the original characters and the intended audience of the source material.
You could write about their first meeting. Maybe Sam was on a hunt and Eileen was also there for some reason. They had a bit of a misunderstanding at first but then realized they were on the same side and started to build a friendship.
In fanfiction, if Sam was kidnapped, it could lead to a very intense story. Dean would surely go on a rampage to find him. Maybe Sam was kidnapped by a powerful demon who wants to use him for some dark ritual. It could also be a new, unknown enemy who has a vendetta against the Winchesters.
Dean is almost always going to be in these fanfictions when Sam is gagged. Their relationship is central to Supernatural. Rowena could also be a character. She might use her magic to either gag Sam for her own purposes or to help him if she has a change of heart. And Gabriel. He could turn up and use his trickster abilities to either put Sam in the gagged situation as a joke or to get him out of a more serious one.
One great fanfiction is 'Sam and Rowena's Unlikely Alliance'. In this story, they team up to face a powerful new threat that the Winchesters alone can't handle. It has a lot of great character development for both Sam and Rowena, showing their complex relationship in a new light. The author does a wonderful job of capturing their voices, making it feel like an extension of the show.
One great fanfiction could be where Dean and Sam have to face a unique Halloween - themed monster. Maybe a witch who uses Halloween traditions to cast powerful spells. They would have to use their wits and hunting skills to stop her before she causes chaos in a small town.
There's this fanfiction called 'Sam and Jack: Unlikely Allies'. It starts with them being at odds with each other, but as the story progresses, they start to understand and respect one another more. The plot is well - paced, and the author does a great job of writing their dialogue in a way that feels natural to their characters.
One great 'Supernatural' fanfiction where Sam is injured is 'Broken Wings'. It delves deep into Sam's struggle to recover after a major injury, and how Dean copes with it. The author does a wonderful job of portraying the emotional turmoil of the characters. It also has some really interesting side plots involving the supernatural elements that we love from the show.