Taken from the Cocktail help manual.
Prebinding repeats the installation step Optimizing System Performance and should be  used if the system has crashed while performing an installation or an update. Prebinding  updates the linking among applications and the shared library files that may be required  to run an application. Whenever a new application is installed, this information needs to be  updated. If the information is not updated, the resolving of these links is calculated when  you launch the application, which takes added time and slows down performance.