Press Alt+F2 to open the run dialog, then type the command to launch your program and prefix it with gksudo (or kdesu for KDE). So for example if you want to open Gedit as root, you run:
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You are asked for your
password and then program will open as root. This limits what accidental stupid things you can do, as only one program is running as root and not all. Aside from the obvious security implications of running as root.
If you insist you want to log in as root, then do so. It's disabled by default but you can allow the system administrator to log in in the Login Window application.