For jeans I think all the girls agreed that plain dark wash denim was essential. Bootcut would probably be most neutral (not thugish or "gay"). I think you should have at least one other option for pants... like beige khakis or a more intresting medium wash denim. But you could probaby get away with only having dark wash.
For shirts it's best to have a bit of everything. Plain white and black ones for days you want to blend, but also some more interesting colours like forest green, burgundy, beige, etc.
I think you will need a slightly more dressy looking shoe to wear with the dress shirts. Jeans are fine, but the shoes are a little too casual - good picks, but casual.
Brands: Adidas is an awesome place to go for mens hoodies and track jackets. It's colourful stuff though if you're okay with that. You can find some awesome and cheap t-shirts and long-sleeved shirts at buffalo. Le chateau also has some great dress shirts for a decent price.