I would never choose a school on the basis of gender. I'd choose a college based on the curriculum it provides in the field I wanted to study. Accreditation is a biggie, too.
Saying that, some disadvantages might be:
Inability to use campus as a dating network (if heterosexual), thus possibly missing out on some of the great college experiences.
Some bosses, when looking at applicants, might judgingly mistake you as something akin to a "femi-nazi" based on you attending a women's college. People are narrow-minded in this world, never forget that.
I agree with Richard Stephen about missing out on differing viewpoints in class discussions. Woman's Study would not have been the same without that diversity of thought.
Syncing periods. (I'm kidding!)