The browser addon, iMacros can be used to automatically click cookies.
Downloading and installing iMacrosEdit
Use the following links to add iMacros to your browser:
Creating and running a clicker macroEdit
Open Cookie Clicker, launch iMacros, and replace the code for the #Current.iim macro with the following:
Run the macro on a loop. Note that you will not be able to leave the page while the macro is running without interrupting the macro.