This script goes over web server log files and sorts IP numbers by number of hits.1
Once you know which IP numbers are causing trouble, you can ask your system administrator to block them. In some cases you might even have a way to block specific IP numbers from a web-based control panel.
Another (less efficient, but sometimes practical) way is to block those IP numbers in your .htaccess file like this:
order allow,deny
deny from 123.45.6.7
deny from …