Baylor
I just received an email from Soulfource, an advocacy group working to end LGBT discrimination by religious institutions. They are about to approach several colleges that have policies against enrolling LGBT students. From their description of The Equality Ride:
In March 2007, fifty-six young activists will board two buses and begin a two month long journey that will take them to thirty-two colleges that have policies banning the enrollment of openly LGBT students.

It turns out that Baylor, which has a Cell Biology department ranked 13 in the nation by U.S. News and World Reports, discriminates against LGBT students. From the email I received:
"Baylor will be guided by the understanding that human sexuality is a gift from the creator God and that the purposes of this gift includes (1) the procreation of human life and (2) the uniting and strengthening of the marital bond in self-giving love. These purposes are to be achieved through heterosexual relationships within marriage. Misuses of God's gift will be understood to include, but not be limited to, sexual abuse, sexual harassment, sexual assault, incest, adultery, fornication and homosexual acts."

More on Baylor from Wikipedia:
Baylor has also been criticized for its policy regarding homosexual students; the student handbook explicitly prohibits homosexual activity, and same-sex partner benefits are not offered to employees. Baylor University is ranked number three on the list of the top 10 "Colleges with Low Acceptance of Gays," a list ranked by students.

The above refers to this list of gay friendly and unfriendly schools.