A common problem with the Security Compliance Manager (SCM) baselines released by Microsoft is that not all settings that you could implement using Group Policy are available in the baselines. You would be able to solve that if you could add settings to existing baselines, or, if you could create your own baselines. Alas!
While not a complete solution, Microsoft has released so-called "setting packs" that at least allow you to partially overcome this problem. The setting packs include the basic information required by the SCM tool to define custom baselines that you can use to create GPO backups, DCM configuration packs, and SCAP content. While you still cannot create baselines for products for which no setting pack is released, at least you can build your own baseline via the setting packs that Microsoft makes available.
For now, setting packs are released for Windows Server 2008 R2, Windows 7, Office 2010 and for Internet Explorer 8. The setting packs for Windows 7 and IE8 are new releases. Let's hope Microsoft soon releases setting packs for the other Products for which baselines are available.
Security Compliance Manager is available at http://www.microsoft.com/scm.