I just remembered: the second chapter of Dengeki Love Machine (also by the Wallflower mangaka) has a story that really fills the bill.

In terms of what you're looking for, Cynical Orange (by the Hush manhwaga) would be absolutely perfect, except for the fact that the beauty in question is female rather than male. But the majority of Hye-Mine's problems stem from the fact that she is attractive. She is naturally not that social, but add in her good looks setting her apart from everybody else, and Hye-Min feels totally alienated from all the other kids at school. She is subjected to rumors, bullying, and sexual harassment from her classmates and has to force herself to make it through school each day.

I totally get why you'd want to look for a manga like this since the vast majority of the time, manga makes being attractive (or popular or rich or really smart, etc.) seem like the greatest thing ever, without ever acknowledging the fact jealousies occur and not everyone will love you for being that much better than them. Vampire Knight, which I mentioned, is kinda like that. Sure there's human students constantly trying to get to their vampire classmates, but it's ultimately laughed off because the pursuers are (weak) humans, and therefore lesser beings.

*Nods* While you can't really say there's not benefits to being attractive, I've always thought the downside to being as attractive as these people are suppose to be aren't really taking very realistic. As you mentioned, jealousy pops up, from people who want to be with them as well as people who aren't considered as attractive. Some of the ones I like take it to the extreme but it does show the down sides, such as the sexual harassment

Though, there's another reason I'm looking for male examples. I've read/watched a lot of harems and everyone treats the guy as lucky for having all these girls after him, even when the women all but rape him. I'm not a guy but unwanted attention is unwanted attention. It's not for this topic but I'm looking for a manga that involves serious sexual harassment/rape of the male that isn't yaoi. It's not all that common that I can find and while you don't deserve to be raped for being gay, or anything, it's kinda saying that the only guys that get raped are gay guys. After Us, A Savage God seems to do a good job of this but I can't find the whole thing

I kinda shy away from the one's involving girls in this role as the beautiful heroine who needs to be protected by the hero is a pretty common theme. Is CO different than that?

Wow, sorry for so long.

Switch Girl!!
Hilarious manga with an interesting storyline. :B

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In the OEL ecchi harem Aoi House, the main character has to make sure his hair doesn't get out of its ponytail, because when it does he transforms into a super-bishounen. For some reason.

I was going to suggest that one myself, and I wouldn't exactly call it shounen-ai other than that one character goes around telling people "I like you" when he really means that he just wants to be friends.

You could try Gakuen Ouji which is a guy in a former all girls school kind of set up but he is harassed by the girls there.

^_^ I love this place. So far I've read almost all of the suggestions and I appreciate everybody who took the time to reply. Drinks on me! Woot!