I am modeling on a set of windows right now, and they are not symmetrical along the X axis, where I need the mirror modifier to mirror the other half of the superstructure. This is what it looks like. The problem basically arises when I need to make the windows non-symmetrical across the mirror.
Solution: Separate the geometry that will be non-symmetrical, and rename it.
Select the object (by right-clicking on it), then press Tab on the keyboard to enter Edit mode.
Then, select the geometry that you want to separate, and press P (hotkey for separating) and you are done!
Now you can press Tab again to go back into Object mode and see the separated geometry.
You can also rename a mesh by selecting it in the Outliner edtior (the object list in the far up-right in the default window layout), double-click the object's name and type in the new name instead of the one with a ".001" at the end given to the object by default.