Change passwords regularly and keep them unique. A strong password has a random combination of letters, numbers, or symbols. Avoid using single names or words found in a dictionary. Never use the names of your relatives, pets, etc. Search the forums for a script supplied by Wizzie that automatically changes passwords. This is a great tool for administrators or multiple sites. There are numerous handy websites that have strong password generators.
Consider using 2 factor authentication
For superusers (and perhaps other powerful users) consider using 2 factor authentication.
Maintain a strong site backup process
Never rely on others' backups. Take responsibility for your backup procedures. Many ISPs state in their contract that you cannot rely solely on their backups.
Monitor crack attempts
VPS and dedicated server users can run TripWire or SAMHAIN. These applications provide exhaustive file checking and reporting functionality, and can be installed in a stealthy manner to help protect themselves in the event of a serious infiltration. (Note: Users of shared servers cannot use this technique.)
Perform automated intrusion detection
Use an Intrusion Prevention/Detection Systems to block/alert on malicious HTTP requests.
There is not a single tool that can protect your site. If there were, it would be so heavily targeted that it would probably become a liability.
Don't reinvent every wheel
Every now and then, hire a professional Joomla! security consultant to review your configurations. Do you remember the adage, "Anyone who acts as their own lawyer has a fool for a client."? The same goes for Web development. Don't expect to catch all of your own security mistakes.