The above link is pretty good - though I very rarely, if ever, let Maya do the cleaning up for me before looking at the problem myself.
The tutorial says that the "select" option (for four-sided faces) is for people who have trouble counting from one to four - but if you have a complex model sometimes the non-quadrangular geometry is easy to miss. Usually cleaning up non-quad geometry is a little more complex than just triangulating a face - I will frequently change a little of my edge-flow when cleaning.
I usually set the cleanup tool to "Select matching geometry", and look for four-sided faces first - correcting areas that don't get selected; then I look for lamina faces and non-manifold geometry.
One "new" feature of Maya 2010 or 2011 (I don't remember which) is that the default selection mode for faces is "entire face" (as opposed to face center) and "pre-selection highlighting". I like to turn them both off. When you set your preferences to select faces by their centers, you'll see little blue dots at the center of the faces. This is really helpful in keeping your geometry clean as you work - you'll instantly see faces with zero geometry area and non-manifold geometry. There is no way to display these when selecting by "whole face".
