• GIO : part of GLib, is the core library used for file and folder operations in GNOME applications
• GVFS: Using GIO with GVFS allows your application to work with files on remote machines as easily as local files.
• GnomeVFS: In previous versions of GNOME, the GnomeVFS library was used for access to files and folders.

source: http://library.gnome.org/devel/platform-overview/stable/gio.html.en

The Difference between GVFS and GnomeVFS:
   in summary GVFS uses fuse library to mount files and folders, but GnomeVFS has its own library and only applications that are gnome-vfs aware are able to see files and folders mounted by gnome-vfs. with gvfs every application in any environment can access them.

for more info refer to: 
http://fosswire.com/post/2007/11/goodbye-gnomevfs-hello-giogvfs/

What is GVFS, GIO, GLIB, GConf, Gstream, etc? Now I’m reading Gnome Documentation Library and I thought this is the start page.

so this is :An Official Guide to Gnome Libraries and Tools.