The application preferences are stored in the MacOSX home directory, or ~/Library/Preferences. Why is this good to know? Well, there are some few cases where an application suddenly won’t start, or if it starts, it has weird values that causes problems. One way, if possible the last one, is to remove the preferences and start fresh.
The preference file should have an indication of the actual application name. You could also double-click on the preference file, and the so called plist editor will open up with information about the preferences. Anyone who knows could even change the values via the plist, but it’s usually good to make a backup of the preference file so you could restore things back in case the application stops working.