A lot has changed since I asked this question in 2012. These days, pkexec is the preferred way to run things as root, as many desktop environments will implement their own frontend (polkit agent) for it, meaning you won't have to bother with checking for different environments. Additionally, gksudo and kdesudo have been deprecated.

Since python 3.5, the proper way to do this would be:

import subprocess

subprocess.run(["pkexec", "<command>", "<arg1>", "<arg2>"])