A very frequent theme is redemption. Peter, especially, has a lot of past wrongs to make up for, and in many fanfictions, his journey towards redemption while interacting with Stiles and Derek is explored. There's also the theme of family. They form an unusual family unit, and how they adapt to that is often a part of the story.
One common theme is self - discovery. Since Derek is a complex character, many fanfictions focus on him learning more about himself. Another theme is friendship. Writers often explore the relationships he has with other characters in the story. Also, adventure is a popular theme. Derek is often put into exciting and dangerous situations in fanfiction.
Common themes would include the power dynamics between Derek and Stiles. Since Derek is in heat, there might be a shift in the power balance in their relationship. There could also be a theme of protection. Stiles might feel the need to protect Derek from potential threats while he's in this state. And of course, love and attraction are likely themes, as the situation could intensify their feelings for each other.
The theme of growth is also prevalent. Stiles may grow in terms of his understanding of Derek and their relationship. He might become more empathetic or stronger in the face of the pain Derek has caused. Derek, on the other hand, might grow in his ability to control his actions and emotions better.
Love and acceptance is also a big theme. They often have to deal with others' opinions of their relationship, whether it's from their friends or the wider supernatural community. And they have to learn to accept each other's flaws and differences as they fall in love. It makes for some really interesting and emotional storylines in the fanfiction.
One common theme is the forced proximity. Since Derek kidnaps Stiles, they are forced to be close to each other. This often leads to a deeper understanding of each other and sometimes the development of romantic feelings.
One common theme is friendship. Since they are often in the same story, their interactions and the growth of their friendship are frequently explored. Another is the supernatural aspect as they are often part of a supernatural world in these fictions.
The theme of self - discovery is also present. Through their relationship, both Stiles and Derek may discover new aspects of themselves, like their capacity for love and vulnerability.
One common theme could be action - packed moments. Stiles jumping on Derek might be part of a fight scene or a sudden, impulsive move during a dangerous situation in the story.
One common theme is the exploration of their hidden desires. Since in the original they might not have had an overtly romantic relationship, fanfiction often delves into what they might be secretly wanting from each other.
A common theme is loyalty. They often have to show loyalty to each other in the face of various threats. For example, in many fanfictions, they are targeted by other supernatural beings, and their loyalty is what keeps them alive.