I prefer to read properties from a source defined outside the program:

java -DMY_APP_CONFIG=~/.myapprc

This way different users can have different config-files.
Even one user may have different ones.

This way the user may put his configurationfile to a place which is part of a backup.
And don't has to unjar the jar, which is discussed above.

Another search-strategie which is well established looks like this:
- is there an explicit configuration-file given? (-DMY_APP_CONFIG=~/.myapp-tiny-rc)
- if not, is a configuration-file found at the users default-place (linux: ~/.myapprc)
- if not, is a system-wide config file available (/etc/myapprc)
- if not, use build-in defaults.

This way, configuration is simple, but fine granulated control solutions are possible.

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