When you type run, you can choose which one of several different configurations you'd like to run.
E.g.run tomcat will run the tomcat configuration
The jboss/conf/tomcat folder just holds all the configuration data for that, erm, configuration.
You can create your own configs by copying the default folder, giving it a new name (say dave), and tweaking the config files inside. You would then start the new config by typing:
You may want to do this to use a different database or try out the server with some other settings for example.