Many people use the term "wireframe", "mockup", and "prototype" interchangeably. I consider a wireframe to be the flowchart that you use to plan out a site's navigation. Mockups are quick sketches that essentially layout the page to show developers where they need to put various objects. Prototypes, then, should be the front-end development of a site that gets handed off to the developer who does all of the behind-the-scenes magic.
Regardless of semantics, essential site creation begins with planning. As I tell my students, if you want to build a house, you don't just go buy a bunch of wood and nails and start hammering pieces together. You need a blueprint that tells you where to put those pieces. I would much rather change a wireframe diagram than an entire site design should navigational issues crop up.
The links below are to various projects that I've worked on that illustrate the various aspects of the prototyping process.