(d)DOS attack
The best way is to have a device installed where your webserver is hosted that analyzes the incomming traffic and then tries to find a pattern in the attacking traffic, then filter that out. The device will have to learn what bad traffic looks like so it may take some time.
These devices are not cheap, but downtime is not cheap either. Look at the big brands like CICSO.
My experience is that it will work over time, but you will probably also filter out some good traffic.. But the bad guys will give up on the attack once they see its not effective any more and then you can disable the device ;)
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