In architecture as in all other operative arts, the end must direct the operation. The end is to build well. Well building hath three conditions. Commodity, firmness, and delight.
Sir Henry Wotton, The Elements of Architecture
THE DESIGN OF THE SITE will determine its organizational framework. At this stage you will make the tactical design decisions about what your audience wants from you, what you wish to say, and how to arrange the content to best meet your audience's needs. Although people will notice the graphic design of your Web pages right away, the overall organization of the site will have the greatest impact on their experience.
The fundamental organizing principle in Web site design is meeting users' needs. Ask yourself what your audience wants, and center your site design on their needs. Many organizations and businesses make the mistake of using their Web sites primarily to describe their administrative organization, and only secondarily do they offer the services, products, and information the average user is seeking. Most readers won't care how your company or department is organized and will be put off if such inside information is all your site appears to offer. Talk to the people who make up your target audience, put yourself in their shoes, and make the items and services they want the most prominent items on the home page.
Notice, in the illustration below, how the major categories in the YaleNew Haven Hospital home page center on the needs and interests of various audiences, not on how the hospital is organized: