Some fanfictions focus on how their marriage affects the rest of the Supernatural universe. For example, how their relationship impacts Sam or other characters. There are also themes related to their different natures - Dean as a human and Castiel as an angel - and how they navigate their married life with these differences, such as Castiel trying to understand human emotions better for the sake of their marriage.
One common theme is friendship. Their bond, whether it's a platonic friendship or something more, is often explored. Writers like to show how they support each other through tough times.
Romantic relationships between them are also a popular theme. Writers might explore how a relationship between an angel (Castiel) and a hunter (Dean) would work, dealing with the differences in their natures, their loyalty to their respective worlds, and how they overcome obstacles to be together.
A common theme is friendship. Often, the stories focus on how the reader becomes friends with Dean and Castiel. Another theme is adventure. Since they are hunters in the Supernatural world, they go on many adventures together with the reader. For instance, they might go on a quest to find a powerful artifact.
One common theme is the exploration of forbidden love. Since Castiel is an angel and Dean is a human, their relationship often goes against the norms of both their worlds. Another theme is sacrifice. They are often willing to sacrifice a great deal for each other.
Love and acceptance are also very common themes. Dean may struggle at first with his feelings for fem Castiel, but eventually comes to accept and love her for who she is. There's also the theme of power. How does fem Castiel's power change or stay the same in relation to Dean? And how do they use their combined powers in different situations, like during hunts or facing off against supernatural enemies.
One common theme is redemption. After Castiel hurts Dean, he often tries to redeem himself, which shows the depth of his love and friendship for Dean.
Another theme is the idea of identity. How does Castiel's female form change her perception of herself and how does Dean view her differently? It can lead to stories that are centered around self - discovery and acceptance. In some fanfictions, Castiel struggles with being in a female body and Dean helps her come to terms with it, which is a really interesting take on their relationship.
Another theme is the struggle between their different natures. Castiel being an angel and Dean being a human hunter. This creates a lot of internal and external conflict in the stories, like in 'The Clash of Worlds' fanfiction where they have to overcome their differences to be together.
One common theme is the contrast between the 50's era and the supernatural world. The 50's had a certain aesthetic and set of values, and when combined with the Supernatural elements, it creates an interesting dynamic. For example, Dean's more modern - day sensibilities might clash with the more conservative 50's society while he's on a hunt with Castiel.
One common theme is the vulnerability of the characters. When either Castiel or Dean is sick, it shows a side of them that is not often seen in the show. They usually rely on each other for support, which is another theme. For example, Dean might take care of Castiel in a more gentle way than he normally shows, and vice versa.