You need to modify two files to enable root login via GDM (Gnome Display Manager) which is the default display manager on Debian 6.
First edit /etc/gdm3/daemon.conf and add the following line:
under the security options i.e. under the [security] tag.
Then comment out the following line in /etc/pam.d/gdm3
auth required pam_succeed_if.so user != root
You should then be able to login as root via GDM.