Migration considerations
If you're still running Windows Server 2003, it might be because you don't know it's there – use the free Microsoft Assessment and Planning toolkit to find out if you have any servers that need replacing. This will also tell you what applications are running on your servers – think of it as a chance to see if you still need all those applications as well as to find out whether you can run the same software on newer versions of Windows Server.
You're definitely going to need new hardware to run a new version of Windows Server; look for a server that has a TPM to get the best security features when you do move to Windows Server 2016. But don't wait until that comes out in 2016 – you need to get off Windows Server 2003 before then.
Running Windows Server 2012 or 2012 R2 is a rather different experience from running Windows Server 2003, but while it's tempting to move only to Windows Server 2008 or 2008 R2, remember that Windows Server 2008 is already out of mainstream support (as of January 2015), so you'll only have to perform another migration soon.
There's an advantage to buying a Windows Server 2012 R2 licence as soon as possible (even if you're planning to use the downgrade rights to run Windows Server 2008 R2 instead of running the latest version) – on August 1, 2015 (according to a Microsoft blog that's since been removed) the cost of Windows Server CALs (the client-use licences you need to buy for users who connect to your servers) will go up by about 13%.
Application compatibility
If you know about your servers and you still haven't updated, it's probably because you don't want to move your apps. Windows Server 2012 R2 has pretty good application compatibility with Windows Server 2003; although it's 64-bit only, most 32-bit applications will still run on it – as long as they don't run in kernel mode or have any 16-bit code. You will need to get new versions of security software and system utilities like backup and management tools though (Windows Server now has Microsoft Defender anti-virus built in).
If you don't have the original software for applications you want to migrate, use tools like AppZero to extract the application, along with its data and settings, and migrate it to the new system. Microsoft has the free online Exchange Server Deployment Assistant that lets you migrate Exchange data to a new server. There are third-party utilities from companies like Dell and Metalogix that can migrate workloads like Exchange, GroupWise, Notes, SharePoint and Project.
Treat the end of Windows Server 2003 as a chance to think about what your business needs its servers for, and do as much automation as possible to simplify the next time you need to update them. Given the popularity of cloud services, if you're only using your server for email and file sharing, you can also think about switching to Office 365 and just having Network Attached Storage in the office for local files. You might even save some money by getting off Windows Server 2003.
