In a nutshell, when you mess with DNS, you mess with the glue that holds the Internet together. And relying on one provider—even one with ginormous infrastructure for hosting DNS like GoDaddy—creates an important Single Point Of Failure.
There is, however, a technical solution that can help keep your organization from becoming collateral damage in an attack like this.
DNSWorking under the assumption that the reader has a cursory understanding of DNS, you already understand about primary and secondary zones.
What you may not realize is that the authority for DNS records is contained within the DNS zone information itself, and that you can readily spoof or publish any authority you'd like as a primary.
With that, you can quickly set up a distributed DNS platform that won't topple if one DNS provider gets crushed by a DDoS.
Stealth DNSStart by moving your primary DNS zone(s) in house. That gives you complete, direct control over your DNS records. You can use anything that complies with RFC-1035, but I like to use ISC BIND, warts and all. The disadvantage of this, however, is that your primary will always the first point of attack for DNS; if that can be disabled or compromised, it's a bigger deal than if a secondary is compromised.
You get around this limitation by protecting the primary with secondaries: advertise the secondary nameservers in places like your domain records, and allow no hosts but the secondaries to communicate with the primary.
The final trick is to change your zone records so that the primary doesn't even get listed in the SOA; pick a secondary, knowing you can readily change the SOA to a different one at need. This results in stealthing your primary DNS zone database.
Multiple Secondary ProvidersThe final step is to utilize secondaries from multiple providers. If your ISP provides free secondary service, utilize it. Use xname.org, buddyns.com, or any of the dozen other free secondary services. Use a paid secondary service from godaddy.com or soliddns.net.
The key is to spread the load around. If one of your providers falls over from a DDoS attack, it's not likely that the other(s) will also be getting attacked at the same time.
Update: If the domain registrar is the one being hosed—and for some reason you've been affected by it—there's nothing you can do but wait out the storm. The domain registrar publishes the connection between your domain name and those carefully configured name servers, and theoretically, that information is already being distributed among the various root servers for the TLD of which your domain is a child. The root servers have been shown to be quite resilient to DDoS attacks, so as long as your registrar has done its job correctly, you shouldn't have a problem. If it hasn't, you're screwed.
Update 2: GoDaddy has announced that it was not an attack, but a problem in their DNS infrastructure. Either way, if your single provider becomes unavailable (for any reason), you're still in trouble.