One of the main themes could be the concept of the magical girl system itself. It might explore how the system is structured and what it means for the girls involved.
Often in such stories, there are supporting characters like the friends or family members of the magical girls. They may not have magical powers but can influence the magical girls' decisions and emotional states. For example, a best friend from school might notice the strange behavior of the magical girl and try to figure out what's going on, adding an extra layer of complexity to the story.
Another theme is time - related. Since Homura has the ability to manipulate time in the show, many fanfictions play with this concept in relation to her relationship with Madoka. For example, stories might involve Homura going back in time to save Madoka in different ways or dealing with the consequences of her time - traveling on their relationship.
Well, shoujo manga is a genre of manga that focuses on the lives and experiences of young girls. It often has beautiful art, emotional storylines, and explores topics like first love, school life, and self-discovery.
I think there are several, but the exact number might change as new ones could be released. You might want to check reliable manga databases or official sources for the most accurate count.