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.