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Plug-ins can add pages to the global preferences dialog when they want to expose global options to users.
For UI guidelines about preference pages, see User Interface Guidelines#The Preference Dialog. The most common problems with preference pages seem to be empty root pages and exposing too many preferences.
Empty Root Pages
Exposing too many options
Plug-ins should try to make decisions for their users. The more configurable options you have, the more do you place the burden of those decisions on the users, and the more complex your code will have to become if it has to support all combinations of possible options. For background, see also this essay about free software and good UIs (scroll down to "The Question of Preferences").