What colleges/universities allow male/female roommates?

Rice does.

Based on research by http://genderblind.org, as of Summer 2008 there were 36 colleges and universities that had opposite-gendered housing options, with most policies having been adopted after 2004. The full list can be found here: http://www.genderblind.org/research.pdf

Stanford does in select dorms (namely Mirrielees, Terra, Castano, Enchanted Broccoli Forest, Branner, and Narnia)

The does, with its gender-neutral housing program: Gender-Neutral Housing Gender-neutral housing is a program that can broaden student's choices and help ensure living arrangements that are welcoming and inclusive for all members of our community. Selected units in Haggett Hall, Poplar Hall and Nordheim Court will be shared by students of any gender, sexual orientation, identity, and expression. Gender-neutral housing is open to any self-nominating student, including but not limited to members of the GSD or Ally community. It is offered as a safe and inclusive alternative for students within the GSD/Ally population. Students who select an apartment in a gender-neutral area will be contacted by the building's Resident Director to ensure mutual understanding of community goals and expectations. If you are interested in living in our gender-neutral housing, please request it on your housing application. Source: https://www.hfs.washington.edu/housing/Default.aspx?id=2391#gsc.tab=0

Duke University too, from Fall semester 2013 onwards.

When I left Harvard, they were just starting to allow males and females in the same suite, provided there was one lockable door between the two.

Apparently Columbia University is allowing this either starting last year or this year or sometime in the near future.

Carnegie Mellon: only in particular "dorms" (off campus Oakland Apartments) when by request of upper classmen

The University of Chicago has it available for students who stay in housing after their first year.