I used to have problem with connecting two objects, because when I smooth the final object, there was a darker line on the connected parts (for example when I was making head, I've had eyes darker this way). Then I found out that I can get rid of it by hitting Ctrl+N, but I don't realy know what it does. I can just see that the lines are gone. So, what does Ctrl+N do?
In future, to find out what tool is being triggered by a shortcut, you can search in the 'Input' section of the 'User Preferences'.
Going to File> User Preferences (Ctrl+Alt+U)> Input, you can use the search field to search for tools assigned to shortcuts. The 'Filter Method' drop down box must also be set to 'Key-binding' for this to work:
This will yield a list of all tools in blender using that shortcut. For example, "ctrl n" would result in showing that that shortcut will 'Make Normals Consistent' for meshes in edit mode. 'Make Normals Consistent' will make sure all faces of the mesh are facing the right way and shaded correctly see: Render has strange artifacts. It also lists other commands that use the same shortcut such as 'Reload Start-up File':
You can also look in the bottom of the toolbar (T) in the 3D view immediately after using the shortcut to see what was triggered:
In Edit mode, which I'm assuming from the information that you are referring to, Ctrl+N recalculates the normals of the object to try to make them consistent. The direction of the normals tells Blender what is the inside and what is the outside of an object.