Back in high school I was big into Target clothes and basically whatever my mom bought for me, because I had video games to play and didn't give a shit. Then I went to college and realized I looked like a fucking nerd (it didn't help that I go to school in Santa Barbara, where all the women are smoking hot and the guys really have to step up their game). So I took some advice from my roommate at the time and bought some new clothes.
As has been mentioned, I feel a very solid look is a good v-neck with some nice shorts. Nothing too long, preferably ending right at the knee.
Tilly's is a good place to shop for both of these. My favorite shirts are what I like to call "covert nerd shirts," or shirts that, if someone doesn't get the reference, won't immediately judge you. For instance, I have a white t-shirt with a big "Aperture Laboratories" logo across the front. If you've played Portal, you'd get the joke and laugh. If you haven't, you'd think "maybe he works there," not "what a fucking nerd."
I won't wear any shoes besides Vans. I've seen Converse and I've seen people wear them and I just don't think they look as good. Mostly just like clown shoes. I've got a pair of white vans for when I wear white shorts, and black vans for my black and brown shorts.
I do my jean shopping from Levi's, and get the slim fit kind. They generally look as good as the $180 pairs from Rockin Republic or Abercrombie, but at $30 and without the holes.
My biggest problem is finding respectable long-sleeve shirts, though I imagine I'll start wearing t-shirts in the winter and get a nice sweater or jacket. Anyone have suggestions on where I can find such clothing?