Are there any where an unpopular boy (doesn't have to be a nerd) and a popular girl fall for each other. Then the guy has to deal with bullying because he's "not good enough" for the girl? 

@fanitha

I don't think Densha Otoko takes place in a school.
When I See You Again- Its similar to what you're asking for. The guy used to be unpopular and was bullied constantly for his looks. He falls for the girl who is popular. But then there's a time-skip and most the story takes place in the future when the guy becomes a rich business man who is now handsome and the girl is a poor motel owner struggling to make ends meet. There are plenty of flashbacks back to past where he was unpopular and she was popular, but like I already said, most of the story takes place in the present.
Uff, idk any of unpopular Boy, but i have one where the Girl is unpopular: Kingyo Club