Yes, it's really annoying. Best way to deal with scan drones and crap with apache?... I must say modsecurity + crs (core rule set). ModSecurity is a web application layer firewall. Modsecurity have tons of rules, you will find the base rules, optional and experimental (there are many third party rules too).
I'm using some rules from the base set. Now in ubuntu 12.04 you can install the module for apache and the core rule set with:
apt-get install modsecurity-crs
To deal with the configuration file can be hard but you will find a recommended configuration file.