One common theme is redemption. The bully or the situation that causes the bullying often gets resolved in a positive way, like the bully realizing their mistake. Another theme is self - discovery. The bullied boy often discovers new aspects of himself through the relationship with the other boy.
One popular bullied boy x boy fanfiction is 'The Unseen Bond'. It tells the story of a shy, bullied boy who finds an unexpected connection with another boy who stands up for him. Their relationship develops gradually as they face the challenges of school and the bullies together.
One that comes to mind is 'Manga X', where the main character, a kemonomimi, faces a lot of bullying. It's got a deep story and interesting characters.
A bullied boy, Sam, was teased for his thick glasses. The bullies would call him names like 'four - eyes'. Sam decided to focus on his studies and became really good at science. Eventually, he won a science competition which made the bullies respect him a little more.