First of all be aware that a lot of computer companies offer really good deal for students through the school bookstore.
As for going for a generic type pc made at a small storefront operation, I'd sat don't.
They can be great systems at a great price but a lot of times these guys that put them together don't know what they're doing and don't back up there work. It's for people who really know hat they are doing and have done the research on each and every component. I've never heard a bad thing about Dell or Gateway.
You're best bet would be to look at PC world (especialy back issues!) and become familiar with all the good and not so good systems.