Microsoft has released wonderful tool SQL Server 2008 R2 Best Practices Analyzer. I have previously used this tool and found it quite helpful. Here is the latest version which you can download from MS site.
Microsoft SQL Server 2008 R2 Best Practices Analyzer
However, I received quite a few emails that users are not able to install it after downloading this tool. There is nothing wrong with this tool but there are two prerequisites which are needed. I am additionally listing the download link to all of them here with.
Microsoft Baseline Configuration Analyzer 2.0
Microsoft PowerShell 2.0
Reference: Pinal Dave (https://blog.sqlauthority.com)