I think the story you are looking for is Evernight by lilrinnieb. She took it down from AFF but you can read it on her website. The story is password protected, so you have to send a friend request and she'll give you the info.
http://lilrinnieb.webs.com/
Is it the story where Harry did a photo shoot for a man's cologne and his dorm mates found the magazine and threw Harry out of the tower because of it? Problem is, I don't remember the title.
Can someone help?
I think the story you are looking for is Meddling in the affairs of wizards by lady.edgecombe.
http://www.fanfiction.net/s/5989687/1/Meddling_in_the_Affairs_of_Wizards
The story you are looking for is A most trusted soldier. There is also a sequel. Click on the author for the profile.
http://www.hpfandom.net/eff/viewstory.php?sid=27063
If you like a dark!Harry, there is The Revelation of the Dark Lord on hpfandom. There is a bit of gore in the story. Not too explicit, but still, so fair warning.
I think the story you are looking for is Tears falling in darkness:year one. It's still a WIP, though.
http://www.fanfiction.net/s/5370271/1/Tears_falling_in_darkness_year_one
I don't know if this is the one you are looking for but it's called Let the guilty pay by Janara. It's a WIP and hasn't been updated in ages. At first Harry is turned into a girl because a potions accident. When he turns back into a boy, it is revealed that he is Draco's twin.
http://www.fanfiction.net/s/3771961/1/Let_The_Guilty_Pay