The .gvfs directory found in home directories of users is actually the GnomeVFS (Gnome Virtual File System).  This provides seamless and uniform access for the Nautilus file manager to  users data no matter where and how it is stored. Data can be stored on a remote mounted file system, the local disk, a USB drive or a digital camera and from the user’s perspective, it is the same.

However, you may get a permission denied when accessing this directory (this is a bug). And even as a superuser/root, you will not be able to enter, delete or change permissions of the directory.  When listing the home directory, you will get

d?????????   ? ?    ?       ?                ? .gvfs

Some applications will fail to execute and you are stuck!  Well, the .gvfs is a filesystem, so you can umount it!

umount /home/<username>/.gvfs
rm –r /home/<username>/.gvfs

You may not want to remove it but once you un-mount it, this should be a safe thing to do (as long as you never had a directory by that name before) but you may want to just check on it.