I know this is kind of a crazy idea but how about 
making cleaning up all these infected machines the priority as a 
solution instead of defending your dns from your infected clients. They not only 
affect you, they affect the rest of us so why should we give you a solution to 
your problem when you don't appear to care about causing problems for the rest 
of us?
 
George Roettger
  Hi,
as 
  a comsequence of a virus diffused in my customer-base, I often receive big 
  bursts of traffic on my DNS servers.
Unluckly, a lot of clients start to 
  bomb my DNSs at a certain hour, so I have a distributed tentative of denial of 
  service. 
I can't blacklist them on my DNSs, because the infected clients 
  are too much.
For this reason, I would like that a DNS could response 
  maximum to 10 queries per second given by every single Ip address.
Anybody 
  knows a solution, just using iptables/netfilter/kernel tuning/BIND tuning, 
  without using any hardware traffic shaper? 
Thanks
Best 
  Regards
Luke