I've been wondering about this for best practices as well.
For what its worth, I have been passing in the name of a properties file as an argument of the topology. There's also a default version that I package with the jar in case there is not a customized version to specify on the command line. For example:
storm jar my.jar my.Topology topo-name config-file-name
I then read in the properties and add them to the Config object so they are available to whatever portion of the topology might need them (spout, bolt, etc).