An administrator or a user with sufficient rights has the possibility to create new sub-sites. He can choose a template and colour theme provided by the organization. You can create for example sub sites for each project. These sites are created from a template and contain automatically the correct layout and content. The sites can have different security then their mother site or children.
There is a possibility to save the site as template, with or without content.
It is possible to create these sites with web services, hence an external application can create these sites. From your site, you could create a new sub site when a new project is launched. Each site has a search functionality that can search the complete content of the site, including the content of the documents. Site content is created with web parts. You can have different web parts, HTML content, pictures list, document library web part (a view on the content of the library), custom web parts, etc.