Here's everything I can remember about the specific story I'm looking for.
Dean wakes up one morning as a woman, and learns it's a curse that can't be broken but will wear off in seven years. So since he's stuck, he chooses to adapt: he keeps his hair short, doesn't shave his legs, takes periods in stride, buys a vibrator, and has lesbian encounters at every opportunity. His biggest hurdle is accepting that he's smaller and physically weaker, and vulnerable in a way he's never been before.
Sam, for his part, has become really protective over Dean like he's never been before. Even Dean's attempts to experiment with men are all blocked because Sam always scares the guys off. Ruby's plans to seduce Sam are thwarted because not only is Sam totally focused on Dean's situation, but he's also struggling with a burgeoning sexual interest in Dean.
There's one scene where a near-rape occurs. Ruby possesses a man, and the man tries to attack and kill Dean. I think it ends with Sam killing Ruby.
Ultimately, Dean and Sam end up together, and the demons play their last card to break things up - they give Dean the answer to breaking the curse (something about a basilisk), hoping making him a man again will reestablish the status quo. It doesn't quite work, because regardless of Dean's gender, the two are in love now.
Any help finding this story would be greatly appreciated.
FOUND in the very first comment. Man, you guys are good! :D