I'm planning on develop a java application to be cross platform. I find out that the settings of a mac application are usually kept in a file named info.plist. By looking for a similar file in my Ubuntu box I found that my applications create hidden folders in the home directory. Is that the only standard?
There is an effort by the (largely ignored, unfortunately) freedesktop.org group to standardize this across Linux desktops:
http://www.freedesktop.org/wiki/Specifications/config-spec
The references on that page, especially at the bottom, should give you some idea of the mess of this landscape.
Also that page is several years old, I believe. Don't hold your breath.