SharePoint data and content is organized and stored within individual sites. A site can be created for a company, department, project, meeting, process or anything else you can come up with. The main point is to think of a site as THE place to go to find all the relevant data, documents and information about a subject. There are a two main reasons why. First, it's easier to secure all related content when they're all located in one site and second, it's easier to find information as well.
When you want to create a new site you'll be presented with many different kinds of site templates. These sites are pre-built with certain types of lists and libraries to help you setup your site quickly. For example the Team Site has a basic list for tasks and a library for shared documents where as the Decision Meeting Workspace has some more specialized lists (agenda and decision) for meetings to track status and make decisions.