One of the reasons why Server Core 2008 is not that popular is because basic configurations have to be made on the command line. Perhaps this alone wouldn't be a problem: however, most of Server Core's commands are somewhat longwinded, at least when you compare this system with other CLI-based operating systems such as Linux. This is why, almost immediately after its release, several Server Core configuration tools came up. The Windows Server 2008 R2 edition of Server Core comes with its own configuration tool: Sconfig.
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You can launch the tool from the command line after logging in. Sconfig allows you to configure the following Server Core settings: Domain/Workgroup, Computer Name, Add a New Local Administrator Account, Configure Remote Management (Allow MMC Remote Management, Enable Windows PowerShell, Allow Server Manager Remote Management, Show Windows Firewall Settings), Windows Update settings (automatic or manual), Download Updates (all or recommended only), Enable Remote Desktop, Network Settings (IP address, DNS server, Clear DNS Settings), date and time, Log Off User, Restart Server, and Shut Down Server.
Sconfig is basically a simple batch script, which is sufficient for these common configuration tasks. The tool supports most of the essential settings. However, a few important configuration options are missing: Windows activation, Firewall settings (Sconfig can only display them), and server role installations.
Therefore, I think third party Server Core configuration still has its right to exist. I am aware of three free Server Core management tools: Server Core Configurator, Core Configurator Console (CCC), and CoreConfigurator. I tried all three tools on Server Core R2 and they still seem to work. Each of the tools has its advantages. CCC has the most features, and CoreConfigurator has the nicest interface. Note that the tool is no longer officially available, but you can still download it here on 4sysops as long as nobody complains. The new commercial version, SmartX CoreConfigurator, has no specific Server Core R2 version at the moment, but I suppose it will work on R2 just like the other three tools.
Sconfig and these tools are needed only to configure the basic settings after the installations. Server Core R2's most important management feature is that it can now be configured remotely with Windows Server 2008 R2 Server Manager. It is also possible to manage the Server 2008 Core with the RSAT MMC tools, but with Server Manager, things become more convenient. Most important is that you can now install server roles remotely.
Other important new features of Server Core R2 include support of a subset of the .NET Framework (2.0, 3.0, 3.5), ASP.NET, Windows PowerShell (including remoting), and support for File Server Resource Manager (FSRM) (managing quotas, file screens, data storage policies, etc.). I believe that together, all of these enhancements will finally bring about Server Core's success. Especially in virtual and cloud environments, Server Core is an interesting option due to its smaller footprint. If you only require a few server roles or web apps, then it is unnecessary to install Windows Server 2008 R2 with a GUI. The fact that you can manage Server Core remotely with GUI tools should be convenient enough in most cases.