One common storyline could be that Henry's sister discovers she has a special power. For example, she might be able to control time like in some 'Once Upon a Time' scenarios. This power could either be a blessing or a curse as she tries to fit into the world of Storybrooke. Another storyline could be her exploring her family history. Since Henry's family has such a complex backstory in the show, she could be on a quest to learn more about her parents and how they came to be in this strange world. And sometimes, she could be involved in a love triangle with some of the other characters in town, adding a romantic and dramatic element to the fanfiction.
Often, she is made into a key figure in saving the town. In 'Once Upon a Time' the town of Storybrooke is constantly in danger. Henry's sister might have a prophecy associated with her that makes her the only one who can stop an incoming evil. She could also befriend some of the villains in the story and try to redeem them. This would create an interesting dynamic as she tries to balance her relationships with the heroes and the villains. Maybe she forms an alliance with the Evil Queen, Regina, and together they work towards a common good, which is a complete turnaround from their initial relationship in the show.
In some fanfictions, Henry's sister is portrayed as an outcast. Despite being related to Henry, she doesn't feel like she belongs in Storybrooke. She might then go on a journey to find her true place. This could lead her to discover other realms that are not part of the regular 'Once Upon a Time' universe. She could meet new characters and bring back knowledge or powers that help in the fight against the darkness that looms over Storybrooke.