Actually the prebinding runs periodically by the system on its own in the background.
If you open a terminal and go to the /var/log/ directory and open up the system.log or just run: tail -100 /var/log/system.log, you might be able to see the last time the system ran the prebinding update.
Basically Johnny G4 is right in that you do not normally need to go and run it yourself. If you notice the system slowing down you can always run it and then reboot.
The biggest files to worry about at the log files that get rotated and the locate db that gets rebuilt. These are run late at night (if you keep your comptuer on overnight) and run by crontab scripts. The biggest thing that these scripts actually do is backup the "local.nidb". This right now is the heart and soul of all your user and system information.
To run these yourself open a terminal and type:
sudo periodic daily weekly monthly
give it a couple of minutes as it starts to run it's course and then you will be given a command prompt at the end and you can exit..