I don't know if you read this yet, but its my all time favorite collegefic of the boys. However, the first one is a one shot and the second part is a movie remake of Superbad, and they are in High School. Then it goes onto summer, THEN college. But it fits your requirements, and if you havent already read it, I highly recommend.

Reinventing Love 'verse - masterpost.
(http://users.livejournal.com/_mournthewicked/195307.html#cutid1)

The Lone Star Showdown (http://paragraph.livejournal.com/52669.html) by paragraph

it features jared hating jensen in highschool for stealing the lead role in the school play, then they end up as roommates in college and romance ensues :) fits right in to your requirements! hope you haven't read this yet :x

#1

It's Not Easy (But It's Worth It) (http://akintay.livejournal.com/139289.html) by akintay
Summary: College AU. Right before the start of his sophomore year Jared finds himself without an apartment and without a roommate when Chad decides to move to California. As it turns out, the real problem isn't finding a new place to live but the fact that, once he does, one of his new housemates seems to hate him. Jared can't figure out what Jensen's problem is – nor why the hell he's crushing on him anyway.

#3

What You Really Really Want (http://kelleigh.livejournal.com/300637.html) by kelleigh
Summary: College doesn't change Jensen and Jared. It only changes what they are to each other. Sequel to That's Not Our Song (http://kelleigh.livejournal.com/282700.html)

#4

18 Years To Life (http://fatebegins.livejournal.com/65313.html) by fatebegins
Summary: Jared is in high school and his boyfriend, Jensen, is in college and Jared finds out that he's pregnant. Jared has to deal with pregnancy and some other things.

This is a fly-by rec post, but here are my fav (http://delicious.com/electricmonk/theme%3Acollege) college J2 AUs. Perhaps you will find something there to your liking. :)