Hold everything, the title of your post got me off-guard once I read your post. So let me clarify... you are in a regular user account and want to execute a graphical app with root powers, right? If so there are several ways, if your are using KDE just run
or type from your console (or konsole again -if you use KDE)
su -c "appyouwannarun"
. Hope this helps.
EDIT: Avoid log in as root.