According to Genesys Supported OS and Databases White paper, W2K is supported starting with G6.1.
We did an upgrade few months back and I do recall a need to make sure if W2K was supported or not by G6.1 products, but I do not think we were affected at all.
There was a single fluke with a softphone application we had that we could not explain, but it looked like it had nothing to do with with OS.
I forgot to mention that we did it using Method 2, because we decided that using a clean OS would get rid of any speculation that a particular problem we are experiencing is caused by improper upgrade.
There is way too many things that are needed to be checked if we were to decide to go with metod#1, because we are using a lot of thirdparty products and we would need to check each one of them on upgraded OS anyway!