Web application: A Web application is an application that can be accessed through the web. Our own Web applications developed with VS are typically manually deployed to IIS, while SharePoint Web applications are automatically deployed when SharePoint is installed (including the creation of databases, the connection of ASP. NET pages to the database, and so on).
and its directory structure is built by SharePoint itself and has its own placement rules, unlike the one we used to define the directory structure for functionality and business needs. (http://www.contoso.com)
site collection: A site collection consists of a top-most site and all the sites under it. It must be built under a Web site application. The site collection that you just created contains only one top-most site. From an architectural standpoint, you must store all the content of a site collection in a single content database. You cannot spread the content of a site collection across multiple content databases. You can create multiple site collections under each site application. such as Http://www.contoso.com/sites/TeamA and Http://www.contoso.com/sites/TeamB.
Web site: A Web site is a recommended virtual concept under a site collection. The site we used to create with ASP. NET is equivalent to a Web application, which is not the same concept as the current site. In SharePoint, a site is a virtual product that is built under a site collection and can contain subsites underneath the site.
The structure looks like this:
Reference: http://www.cnblogs.com/iamlilinfeng/p/3186919.html
Http://technet.microsoft.com/zh-cn/library/cc262410.aspx