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The main difference is the name of the issuing authority as shown in the root certificate. If someone were to inspect your certificate, they would see “Go Daddy Class 2 Certification Authority Root Certificate”. I suppose it depends on how much confidence your users would place in this name. Security paranoids would have the root certs installed already, low level users probably wouldn’t even know such a thing existed, but mid-level “power” users who haven’t heard of GoDaddy might be suspicious (or at least more so than say VeriSign for example).
Technically speaking there is not much difference – they are all standard X.509 certificates. I generally find that if you can get the cert in .PFX format (with the private key embedded) it works well across platforms. If you can only get another format (.cer) it’s fairly straightforward to convert it using the Certificates snap-in in Microsoft Management Console.