Both fairly long, although one was epic. The first was many, many chapters. Jensen was the RA in Jared's building, he formerly had a relationship with Justin, who cheated on him, then he winds up with freshman Jared. At one point, Jensen totally freaks out after a conversation with Jeff, and dumps Jared, but they get back together. A number of the chapters that follow up with Jared's sophomore year of school focus on other couples/characters, including an involved storyline where Steve was in love with Christian, but winds up later with Justin.
I can remember all this, and not the title or author!
I remember fewer details about the second fic. I do remember that Jared and Jensen were roommates in college, that they get together, and then Jared comes out to his parents, and that doesn't go well. I seem to recall that Jensen may have tried to commit suicide at some point, before the story begins. I also remember that the last chapter I read had the boys going away for spring break, where they ran into an old friend or girlfriend of Jensen's.
Thanks to anyone who can help me find these fics!