Why is harem a common theme in manga/anime? Harem manga and anime are so popular that they have their own category. It's easy to name a few: Girls Wild, High School DxD, Sekirei, The World God Only Knows.

Why is this such a popular theme in both anime/manga? It is odd because in fantasy literature, American cinema, and Western television, harem is not a common theme and would offend most. How is it that they are so extremely prevalent (and seemingly accepted) in anime/manga?
The target audience of "harem" shows is adolescent males - teenage boys. The main character is usually a male high school or cram school student, who is awkward around girls - someone the target audience can relate to, as they are in the same phase of their lives, struggling with love. (Who hasn't?)

Adolescent males have always been a large part of the audience for anime; shows featuring giant robots appeal to the same group. So it's a trope that appeals to the traditional audience.

I'm not sure why we don't seem to have "harem series" in superhero comics, as it could be successful for the same reason. One reason could be that the iconic superheroes like Superman and Batman are already mature, at an age where they are more confident around females, and also expected to behave more maturely than the protagonists of harem series.