1) Non-magic AU. James is alive and is someone high up in goverment, maybe an ambassador to a different country or something like that. Harry is a bit wild, staying out all night, parties etc. James gets letters threatening Harry's safety and hires a bodyguard for him, the take no-nonsense Severus Snape. Harry tries his best to seduce him to save him from boredom, but he hadn't counted on Snape actually falling for it! Bonus points if everyone thinks Harry has been very promiscous but he's in fact a virgin ;)
2)Fifth year, chan. During Occlumency Snape discovers what Dolores Umbridge has been doing to Harry in detention, it turns out her blood quill does other things. Sexual abuse by Umbridge. Snape is torn because he fancies Harry but he doesn't want to take advantage of him. Up to the author whether or not he actually acts on those feelings while Harry is still a student or does he wait?
3) As a child, Petunia used to dress Harry up in girl's clothes as a punishment. The trouble is, Harry liked wearing the dresses but knows such a thing is unacceptable in the wizarding world so he tries to forget about it. But the urges won't go away, what happens when Snape catches up wearing a dress one night? School age Harry, 8th year if chan is not your thing.
4) "People change in the maze". Chan, during GOF. Harry returns from the graveyard bloodied and torn, with Cedric's body. After Madam Pomfrey's medical, she ascertains that Harry has been raped and is now pregnant. Everyone thinks that Voldemort raped Harry that night, but it was in fact Cedric. Harry doesn't know what to do or who to turn to. Who would believe him? Snape finds him crying one night in the Astronomy Tower. Can be a mentor or slash fic.
5) Crossover with House. After the final battle, Harry is suffering from a mysterious illness that no wizard can either identify or find a cure for. In steps renowned Potion Master Severus Snape to the rescue, only he can't figure it out either. Hermione has heard of a Muggle doctor called House in the US and arranges for Harry to get treatment at his hospital. Snape insists on going along, for he doesn't believe a Muggle will be able to help. During Harry's treatment, Snape falls in love with Harry.