During a denial of service attack the website should send the requestor a code to enter to verify a person is actually there. If the correct code is not answered within an allotted amount of time, say 5 minutes, the computers IP address is added to a list of computers to block. This would quickly eliminate bad traffic.
Also, the bad IP addresses should be stored in a central location where other websites can access the list.
Lastly, emails should be sent to the computers that were being controlled for the denial of service attack informing them to contact their ISP and get their computer Antivirus updsted.