incase you didn't know, godaddy has just been hit by some idiot hacker that has caused millions (including my own) sites to go down. This leads me to my question... I was using the godaddy nameservers (NS12.DOMAINCONTROL and NS13.DOMAINCONTROL.COM) for my domain... If I had only registered my domain with godaddy but used different nameservers, then would my site not have been effected?.. i.e. should I consider using diff nameservers?
As you suspect, your domain would NOT have gone down if you had been using different nameservers. Let's clarify some terminalogy a bit:
How to prevent down time if domain registrar goes down?
Your domain will not go down when your registrar goes down. It only went down because you happened to use the same company acting in two different roles at the same time: as a registrar and also a name service provider.
Everything will work fine while your registrar is down except that you probably won't be able to make changes to your domain's delegation or WHOIS data.
How to prevent down time if domain registry goes down?
Again, that won't happen. The registry is just a database. Registrars populate the database and it in turn populates the gTLD or ccTLD nameservers.
Again, you probably just won't be able to make changes while it's down.
BUT! Note that in many cases the domain registry and nameserver operator might be the same entity, so see the next paragraph.
How to prevent down time if parent domain's nameservers go down?
(e.g. your domain is "example.com" and the nameservers for "com" have gone down.)
Answer: you don't. It's down!
But the nameserver clusters for all of the gTLDs (com., net., org., etc...) and most respectable ccTLDs (ca., jp., fr., etc...) are pretty robust and very well distributed. They don't exactly go down often (or at all).
How to prevent down time if domain's own nameservers go down?
You don't, but hopefully you have at least two (or three, or more) nameservers hosting your domain and they won't all go down at the same time.