Basically, they are thinking about style, heirarchical associations, how the eye draws across the page, basic graphic art and design principles but specifically applied to presenting information on the web. A good analogy is to a cartographer (map maker).

They look for patterns and then create maps or blueprints to help people reach their goals through Web interfaces. It is not just about organizing information, but getting people to that information.

Organization methods:
Heirarchical: based on a top to bottom prioritization, parent/child relationship
Taxonomy: Classification according to type. Such as animals, plants, days of the week