How do I run BeyondCompare in X11 as root?
I haven't used WineBottler, but I'm assuming it creates an icon for the app in your Applications folder.

To run any App in OS X as sudo, open Terminal and enter the following:

sudo open -n $foo


Then drag the icon for the App from Finder into Terminal (replacing $foo in the example above). Press Enter and type your password. Voilà! Terminal launches the App as root.

Note that open -n works in Terminal to launch any $foo.app as if it were launched via the Finder. (Otherwise it's impossible to launch and OS X app via Terminal as Apps are really just specialized directories on the filesystem-level.)


  We trust you have received the usual lecture from the local System
  Administrator. It usually boils down to these three things:

#1) Respect the privacy of others.
#2) Think before you type.
#3) With great power comes great responsibility.



( I couldn't resist :P )