The most common role for a server running the Windows Server 2003 operating system is file server. Should you not be interested in upgrading your file servers to Windows Server 2012 R2, you could consider the possibility of migrating your file servers to Samba on Linux.
There is a fair amount of documentation available on the steps you can take to add a file server running Samba on Linux to an existing domain. Most organizations don’t spend much time configuring the advanced properties and capabilities of file servers. If you organization needs something fairly basic to replace a server running Server 2003 as a file server, it might be that Samba on Linux fits the bill. Microsoft has even been contributing open source code to Samba and it wouldn’t be surprising, given Microsoft’s new approach of playing well with others, if Samba on Linux becomes something that’s even easier to integrate into an existing Windows based network.
It’s even possible to create your own domain using Samba based domain controllers. Whether this is practical depends on the features of Active Directory that your organization uses. Samba does most of the basics, but if your organization is using more advanced Active Directory features, you’re going to still need to keep Windows Server domain controller around.