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Good article with good examples of good ways to manage complex interfaces: Managing UI Complexity by Brandon Walkin.

My favorite example might be Microsoft Expression Blend vs Adobe Lightroom.

Some compelling examples are the inspectors in Microsoft Expression Blend and Adobe Lightroom. While a host of factors are responsible for the Expression Blend inspector looking considerably more complex than the Lightroom inspector, the rough horizontal alignment is certainly a primary one. The horizontal alignment lines have been drawn in red to illustrate the differences.

Looking at the red lines, my first thought: “jebus.”