One common theme is adventure. Since John Watson is often associated with Sherlock Holmes and their detective work, the fanfictions might involve the reader going on adventures with him, solving mysteries. Another theme is romance, of course, as it's 'x reader' so there's usually a romantic element between the reader and John Watson.
A frequent theme is friendship evolving into something more. The stories may start with the reader being friends with John, and then as they go through various situations together, feelings of love start to develop. Also, there's often the theme of healing. Given John's past traumas, the reader might play a role in helping him heal, and that forms the basis of their relationship in the fanfiction.
One common theme is the deepening of their friendship. Many fanfictions explore how they become closer and more reliant on each other over time. Another theme is mystery - solving together. They are often depicted as an unbeatable team in solving complex cases. And of course, there's the theme of loyalty. Their loyalty to each other is a central aspect in a lot of these fanfictions.
Often, there's a theme of using his skills. His medical knowledge and deductive reasoning are put to use in the Avengers' context. Also, there can be a theme of culture clash. John Watson comes from a different sort of world in the Sherlock Holmes stories, and his values and ways of doing things might clash or blend with the Avengers' way of life.
One common theme is the exploration of gender roles. Since John is female in these fictions, it often looks at how she navigates a world that was originally male - dominated in the Sherlock Holmes canon. Another theme is relationships, like her friendship with Sherlock or potential romantic relationships. Also, the theme of her proving herself in a male - dominated field, such as detective work, is quite prevalent.
One common theme is friendship. Writers often explore how an original character can form a deep and meaningful friendship with Watson. It could be a friendship that helps Watson through tough times or one that adds a new dimension to his life.
One common theme is the struggle with identity. As a vampire, John has to reconcile his new vampiric self with his old identity as a doctor and a friend. Another theme is the relationship with Sherlock. It often becomes more intense and complicated due to his vampiric nature.
One common theme is the unspoken attraction. In these fanfictions, there's often a lot of tension between Holmes and Watson because they can't immediately act on their feelings. Another theme is loyalty, which is a big part of their relationship in the original stories and is intensified in the yaoi versions.
One common theme is the idea of protection. John is often portrayed as a protector in these fics, shielding the reader from the dangers of the supernatural world. Another theme is the healing power of love. Their relationship is shown to help both John and the reader deal with their past traumas.
One common theme is adventure. Given John Egbert's nature in the original work, fanfictions often involve the reader joining him on various adventures. Another theme is friendship - turned - love, where the relationship starts as a friendly acquaintance and gradually develops into a romantic one.
One common theme is friendship. Their bond is often explored in great depth, like how they rely on each other in difficult situations. Another is loyalty. Fanfictions usually show how they are always there for one another no matter what. For example, in some stories, Watson stays by Sherlock's side even when others turn against him.
You can try fanfiction websites like Archive of Our Own (AO3). It has a large collection of fanfictions, and you can easily search for 'john watson x reader' ones. There are also other platforms like FanFiction.net, but AO3 is known for its wide variety and tagging system that helps you find exactly what you're looking for.