Windows 2008 is highly recommended now. Windows Server 2008, has some great new features and technologies, of course which were not available in Windows Server 2003. Windows 2008 has more inbuilt components as well. Adding to this is the Virtualization i.e Hyper-V which was made available with it.
If your company is completely satisfied with the status of Windows Server 2003 and does not have any pressing need for any of the new features in Windows Server 2008, stay the course and save some money. An upgrade of systems and servers requires much planning and a good deal of money.
You can go with the 2003 version if you need to save money, but the 2008 version is now the industry standard (until the next version comes out). It's also a bit harder to troubleshoot problems with the 2003 version as most new IT employees are trained on 2008.
Regretfully, we are currently running 2003. An upgrade to 2008 would be cost effective in the long run, but our capital just isn't up to it, just yet. Hopefully within the next year we can see a slight rise in business and the economy and upgrade. 2008 is much more stable, easier to troubleshoot, but still has it's flaws.
What server will be better Windows 2003 or Windows 2008?
windows server 2008 one gets advanced features which are not present in windows server 2003 like it has native ip-stack is ver6, mmc differs from windows server 2003.