If one has less exposure on Windows 2003/2008 OS, it will be preferred to go for Windows 2008, as Windows 2003 is getting out of the market place,after some days getting support for 2003 can become a bit difficult as every one is going with the new technology, so its better to start with the latest technology available. Windows 2008 is much more easier and secured, Like configuring Security, use of IPv6, Managing the Domain environment and much more, are supported very well. So I would suggest to go with Windows 2008.
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