If you go to /home/[username] and type ls -a, you will see a ton of folders that begin with a period. These are where programs usually store their configuration information. Because Linux was designed as a multi-user system, the programs tend to be designed to store information in a multi-user-friendly way, which means not assuming the will all want the same thing. Configuration files (sort of like the old DOS .ini files) can also be stored in the program directory for global settings that should affect all users.