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I would tend to use absolute positions more often than margins, but it does depend on what exactly is trying to be achieved. For a liquid layout, margins are quite important, but for positioning an element on a page, an absolute position is more accurate.
It's good practice to try out methods for yourself on dummy pages until you find something that works for you, before you dive into your project for real.
I inherited one site that had over 50 separate elements on a page, all positioned absolutely relative to the BODY element. What a labor that page builder must have gone through finding all those x,y cordinates! But the page was almost all images and it made a kind of sense to put the slices together that way.
A more liquid layout -- one that uses padding, margins, etc -- has proved the most practical for me so far. Absolute positioning on a grand scale tends to buld up the size of the code. You need either a separate ID for each element or you need inline style attributes for each element, and it can create a maintenance hell.
Plus, if there is text involved, a user stylesheet override could cause a major mess.
Personally I lean toward a mixture of the two. I like to absolutely position elements like left/right navigation and then give the content area margin/padding to compensate for the space taken by the nav element.
This creates a semi-fluid design with one or two elements fixed and the rest liquid.