Most casual users are unaware of the fact that there is a command line program to edit almost all system preferences. This program, called defaults accesses the Mac OS X preferences system, and can read and write the values set by any application. Normally, this would be of no interest to the casual user, except that some programs read settings that they display no GUI for, and so your only access to those (sometimes quite useful) settings is through the defaults command.
Note that defaults makes no attempt to notify a running app of changes to a setting, so in order to see your changes, you need to quit and restart the app. Some apps will resave their settings on quit, so in most cases, it is desirable to quit the application before changing the settings, and then restart it afterwards. In a few cases, such as the Finder or the Dock, which are not easy to quit, one must resort to forcibly quitting the application (after which the system will restart it) after applying new settings, usually using the command killall ApplicationName. Note that when an application is killed, it is not given the option to save any of its current documents or settings, so you will not overwrite the new settings, but you may also lose some status (eg. minimized windows in the Dock may unminimize, and open Finder windows will likely be forgotten).
The defaults command has three general types of things it can do that will be useful to us: read, write, and delete. read allows you to inspect the current settings, write allows you to apply your own settings, and delete removes settings from the system which should cause the application to revert to the default for that setting.
To get started, you'll need an open Terminal window. The general form of the syntax isdefaults action domain key [value]
where the things in italics are things you need to fill in with your desired option. The action as discussed in the previous paragraph. The domain is an identifier that says which application to modify the settings for. An example would be com.apple.finder which corresponds to the Finder. The key is the name of the setting you want to change. And you only need to give a value if you are using defaults write, in which case that is the new value to set.
Now that you've got the basics down, you should check out one of the other articles:
Hidden Prefs in the Finder