A Web site is a related collection of World Wide Web (WWW) files that includes a beginning file called a home page. A company or an individual tells you how to get to their Web site by giving you the address of their home page. From the home page, you can get to all the other pages on their site. For example, the Web site for IBM has the home page address of http://www.ibm.com. (The home page address actually includes a specific file name like index.html but, as in IBM's case, when a standard default name is set up, users don't have to enter the file name.) IBM's home page address leads to thousands of pages. (But a Web site can also be just a few pages.)
Since site implies a geographic place, a Web site can be confused with a Web server. A server is a computer that holds the files for one or more sites. A very large Web site may be spread over a number of servers in different geographic locations. IBM is a good example; its Web site consists of thousands of files spread out over many servers in world-wide locations. But a more typical example is probably the site you are looking at, whatis.com. We reside on a commercial space provider's server with a number of other sites that have nothing to do with Internet glossaries.
A synonym and less frequently used term for Web site is "Web presence." That term seems to better express the idea that a site is not tied to specific geographic location, but is "somewhere in cyberspace." However, "Web site" seems to be used much more frequently.
You can have multiple Web sites that cross-link to files on each others' sites or even share the same files.