There are many way to store configuration information in WSS, but you can use the hierachical object store (SPPersistedObject Class).
This class provides the methods for an object to automatically serialize its state, persist that state in a permanent store, retrieve it at a later time, and deserialize it back into an in-memory object.
It is explained on http://msdn2.microsoft.com/en-us/library/microsoft.sharepoint.administration.sppersistedobject.aspx and here http://www.bluedoglimited.com/SharePointThoughts/ViewPost.aspx?ID=271

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