The GIS Data view is split into half. The upper half contains the list of currently loaded projects. See Tracks, Waypoints & Co to learn more about the GIS Data Workspace in general.
The lower half is the database list. A database is a single file that holds your data like a file system with a few advantages. The data in the database is grouped in folders. Blue folders are for grouping several projects. Green folders are like projects. Think of them like a GPX file. The orange folders are like projects, too. Usually you want to use them to keep some secondary data below a green folder.
Whereas blue folders are just to structure data in the database, the green and orange ones can be loaded like files into the workspace. Different to files it is also possible to load just single selected items into the workspace.
As another difference to a filesystem items are not stored in several files. The are just stored once and linked to several folders. Therefore if you edit an item in one project the changes will apply to all other locations the item is referenced. If you do not want this, you have to clone the item. A clone is a completely independent copy of an item.
This applies to a single database. You can load several databases. If you copy an item from one database to another the copies are as well independent as a clone within the same database.