This is an age-old question. Lots of money has been spent on it. LOTS. Studies, special scholarships, etc. Some of it may have to do with spatial relations--especially in mechanical and civil (NOT environmental) engineering; ON AVERAGE, women score much lower on spatial relations tests than men. That said, women actually score slightly BETTER on algebraic math tests than men--but in a very algebraic/calculus-based field like EE, you still see few women. Go figure.
Personally, I've been through eight and a half years of engineering school. I'm defending my dissertation today (2pm... wish me luck!). I've known some VERY good women engineers/mathematicians/computer scientists. They are rare, however. Some of it I would attribute to the "old school" mentality of some of the professors... but I think that's waning. A lot of the newer professors don't care if you're male/female/white/black/asian/purple/pink-with-yellow-polka-dots as long as you're motivated and want to be studying the material. There are a LOT of people, however, who are initially attracted to engineering (esp. in the 90s) because of the high starting salaries and the "job prospects"--and they dropped out because 1) they didn't like the material or 2) saw their buddies in business school doing half the amount of work, and decided it wasn't worth it. This is men and women--but I have seen a lot of women who went into ME/EE (especially these two) because of "minority scholarships" who "dropped out", not because they couldn't hack it, but because they really hated the work. I know the department I'm in added a bio option, and the number of women in the dept doubled in three years. Women, for some reason, are VERY drawn to the medical/humanitarian fields (as opposed to the computer circuit or "blow crap up" fields of EE and ME). Look at the highest enrollments of women in engineering majors... its bio, environmental, chemical (MANY go on to med school/pharmaceuticals). Maybe they find the "good old boys" clubs of EE and ME distasteful. I have no idea. Personally, I don't care what the female enrollment is--whether its 90% or 10%--as long as they want to be there and its what they want to do. Same goes for the male students.
One possibility (that my fiancee proposed--she's a BS/MS in Engineering Mechanics)--engineering is a VERY difficult field to get out of and then get back into. So women who are looking to start a family find that difficult--they can get a GREAT job after graduation, but if they want to "sit out" for five years to have a pair of children, its difficult to get back into the game. Which I can certainly understand. This is also an attributed reason for the low number of women PhDs in ANY field--who wants to still be poor and in school at 27 or even 30? Some women (and men!) view their home life more importantly.
Thats just my $0.02 (ok, maybe its like $10).