There are a variety of ways you can deal with your situation. A combination of the following would be the best solution.
1) Bandwidth mitigation by proxyshield or prolexic and hoping the attackers disappear or stop
2) Removing the root cause of the problem using www.stopddos.org to track the source of the botnet (command and control zone(s) & dns servers) and remove them.
3) Inspect packet logs using tcpdumps and apache access logs to work out what type of attack it is, and build your own custom firewall solutions using something like iptables
Good luck with your decision and I hope the DDoS stops soon.
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