It's mostly the main font and the background, but also the color of some links, textfields, borders, and buttons. Currently each style has its own style sheet. However, it would be worthwhile to have a master stylesheet of the CSS that doesn't change, and individual stylesheets for the custom aspects. If we did that, it would be one big step in the direction of something you are talking about.
insomniasexx is working on a CSS project, which will be done soon. After that, I think we should implement that kind of CSS organization. If we had a handful of customizable aspects, it wouldn't be too difficult to allow for individual customization which would be pretty lightweight.