gvfs-trash is part of GNOME's Gvfs, while trash-cli is a separate set of tools independent of the desktop environment. Both programs implement the XDG Trash specificationXDG Trash specification and should be compatible with each other. For example, you can trash files with gvfs-trash or GNOME Nautilus, then restore from trash-restore or KDE.
update dead link (different site, but same contents)