To me, what makes a nerdy or geeky girl so attractive are three things.
1) Brains. This cashes out in lots of different ways. For me it's common interests (computers, science, sci-fi, etc.), and the fact that usually I can have really good, deep, interesting conversations about things with a geeky or nerdy girl. Some of the best female non-girlfriend friends I've had have been nerdy/geeky girls.
2) An unassumingness to them. Usually they're not aware of their own attractiveness, and those that are very physically and otherwise attractive underneath the appearances to the contrary often don't think of themselves that way, which makes them all the more attractive. I've found that it also makes it more special and important to them when I express my appreciation for their attractiveness.
3) Naturalness. This is a lot like 2) above, but I think of this more as the way they dress and the effort they put into their appearance. I really prefer women who wear little if any makeup, and/or don't spend a lot of time worrying about what they look like. You know, jeans and sweaters kinds of girls... The benefit of this is when they do get all dressed up, they really can blow you away with how they look. My wife always stuns me anew each time she gets dressed up...
Note, I'm not talking about the image or illusion of geekiness that is a Hollywood creation that was mentioned earlier. You can spot those kinds of posers a mile away. I'm talking about real women who are like this. My wife is a perfect example of a nerdy/geeky woman. When we met in college it was through a campus club social function. We had lots of nerdy interests in common; photography, computers, science, etc. She was majoring in biology and computer science. Now she's a systems administrator for the university where I'm a grad student. I'm pretty nerdy, but she can out-hack, out-script, out-program, and out think me on lots of things. Thank god I decided to become a vision scientist, so there's actually some things I can do better than she can!
