In the standard notebook front end,
Mathematica allows you to set a large number of global options. The values of all these options are by default saved in a "preferences file", and are automatically reused when you run
Mathematica again. These options include all the settings which can be made using the
Preferences dialog.
You can access global front end options from the kernel by using
Options[$FrontEnd, name]. But more often, you will want to access these options interactively using the Option Inspector in the front end.