as of version 3.3.1 you can now run Cookie without any visible ui.
i.e. no menubar, and no dock icon.
to enable it:
open up Terminal.app
paste in this command:
defaults write com.sweetpproductions.Cookie canRunHeadless YES
then enable the options: "Show Cookie in Menubar"
"and Hide Dock icon"
depending on which operating system you are running, you may need to restart Cookie for the change to take effect.
to access Cookie you will now need to open it from the Finder. (by double clicking)
To get your ui back, use this command:
defaults write com.sweetpproductions.Cookie canRunHeadless NO