One common theme is self - discovery. The OCs often have to figure out who they are in the context of the Madoka Magica world, which is full of complex rules and moral gray areas.
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.
In Madoka x Homura fanfiction, the power dynamics between them can be an interesting aspect. Madoka, as a very powerful magical girl, and Homura, with her time - looping abilities, have a unique relationship. Fanfiction could play with how they use their powers in relation to each other. Maybe in a fan - created scenario, they combine their powers to save a new threat that wasn't in the original series.
You can start by looking on fanfic platforms like Archive of Our Own (AO3). It has a large collection of Madoka Magica fanfics and you can sort them by popularity, ratings, etc. Another way is to join Madoka Magica fan communities on social media platforms like Reddit or Discord. People there often share and recommend their favorite fanfics.
A fanfic might explore the relationship between Kyoko and Sayaka in terms of their emotional support for each other. Sayaka, after going through a lot of emotional turmoil due to her unrequited love and the harsh reality of being a magical girl, could find solace in Kyoko. Kyoko, who has her own set of traumas, might open up to Sayaka as well. They could have heart - to - heart conversations in a quiet corner of the city, away from the chaos of witch battles, and this could strengthen their bond.
One popular trope is the 'time - loop fix - it' where Homura uses her time - looping abilities to try and create a perfect situation for Madoka. This often involves Homura going through multiple loops, each time learning more about Madoka and how to protect her better.
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, in 'madoka magica side story', it shows more about the hidden secrets in the world of magical girls. For example, it might focus on a particular magical girl's struggle that wasn't fully explored in the main story. It could also introduce new magical elements or enemies that the girls have to face, which adds more depth to the overall story.