With Visual Studio 2012 and the use of SSDT technology, there is only one type of database project : SQL Server Database Project.

With Visual Studio 2010, we used to have SQL Server 2008 Server Project which we used to define server-level objects, mostly logins and linked servers. A convenient wizard allowed for creation of this type of projects. It does not exists anymore. Here is how to create an equivalent of the SQL Server 2008 Server Project  with Visual Studio 2012:

• Create a new SQL Server Database Project : it will be created empty
• Create a new SQL Schema Compare ( SQL menu item > Schema Compare > New Schema Comparison )
• As a source, select any database on the SQL server you want to mimic
• Set the target to be your newly Database Project
• In the Schema Compare options (cog-like icon), Object Types pane, set the options as below. You might want to tweak those and select only the object types you want. Then, run the comparison, review and select your changes and apply them to the project.