A big part of custom web site design is in the field of what is called information architecture. Information architecture refers to structuring information and content based on a logical and consistent navigational concept. It may be simple at first sight but it remains the biggest challenge in custom web site design. As opposed to a "table of contents", an "index", and "chapters" in a book, a custom web web site design does not handle this linear concept in quite the same way. Regarding website navigation, there are three basic types. Global, Parallel and local.
Another advantage of custom web site design is the absolute flexibility to respond to changing environments of vogue visual popularity and changing technologies. For example, using visual metaphors that change periodically to hold a returning visitors interest in new material that demonstrates an evolution of knowledge. This would encourage visitors to click deeper into your custom web site design and become a committed return visitor, and possibly a consumer of your product or service. Visual metaphors should lead to written material that edges you toward the goal of being a reference or authority site.
Web Site Design vs. Website Design
Essentially, there is not much difference between them. They both are used interchangeably by the web community until sometime in the near future when one of them becomes the standard.