Certainly it is an interesting question that I am not certain how to answer. What I see in my home directory are a number of hidden subdirectories. These hidden subdirectories are often associated with personal configurations for various applications and/or applications that I have installed on an individual, instead of system, level.
Over the years I have been seeing the use of these hidden sub-directories increase. A quick look at what is in my home directory leads me to believe that some commonality between Linux distributions does not necessarily exist. It really depends on the application of choice. That is, if I use Banshee in both Fedora and Ubuntu, I would expect that I would have similar configuration files.
I am not certain this this response has actually answered your question. Perhaps a better answer might be: "It depends".