Microsoft Assessment and Planning Toolkit should do the trick.
MAP performs a detailed analysis of hardware for migration to Windows 8, Windows 7, Windows Server 2012, Windows Server 2008 R2, SQL Server 2012, SQL Server 2008 R2, Microsoft Office 2010, and Office 365.
It specifically mentions SQL 2012 at some point, but I guess the same would work for older versions2008 R2 aswell:
Discovery of SQL Server 2012 databases, instances, and selected characteristics.
And here it says:
Detailed reporting:
Covers specific SQL Server instances that include component name, version, edition, and more. Includes wide-ranging details of databases and server instances that can be used for consolidation.