As many BizTalk developers we've been using the SSO (Single Sign On) database for more than just SSO. We've been storing configuration data in that database too. This used to be a work around, and we were using some custom tool to edit the entries in the SSO database. However, we recently learned that Microsoft has release an MMC snap-in to manage the values. You can download it here. Microsoft itself states this about the tool:

This tool provides the ability to add and manage applications, add and manage key value pairs, as well as import and export configuration applications so that they can be deployed to different environments.

That apparently means that even Redmond has "officially" accepted that SSO is used for configuration as well.