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There are a number of ways to do this.
The simplest is just to use su - root and then run the command.
The way RedHat does it is they symlink the program name to consolehelper in /usr/bin They then have a file in /etc/security/console.apps called the name, redcarpet, of the program that contains something like
USER=root
PROGRAM=/usr/sbin/redcarpet
SESSION=true
So that when when you run redcarpet it really runs consolehelper that realizes you want to run redcarpet. It looks in the file, finds the correct path, gives you a prompt and if correct executes it as root for you.
If you are using an alternative form of authiecation, aka something other than passwd/shadow, then you will probably also want to setup a /etc/pam.d file called the name of the program.
You shouldn't have problems with X permissions when doing either of the above, but if you do you can use xhost +localhost to give all local users permission to open things to the current X session.
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