I just installed the latest QGIS development version (build 1.9.90-Alpha), and one of the changes I noticed was the option “Control rendering order” in the layers pane. I had to Google to check out what this new option was about. As Darren Cope explains in his blog, it allows you to decouple the way layers are organized in the legend (“Layers” pane) from the order they are rendered (drawn) on the canvas (controlled via the “Layer order” pane.).
As you can see in the screen-shot above, you can select whether the order of the layers in the ‘Layer’ pane or in the ‘Layer order’ pane determines the order the layers are displayed on the canvas. Could be an interesting option when working with complex maps with many layers.