Change the stacking order for selected layers

The vertical arrangement of layers in the Timeline panel is the layer stacking order, which is directly related to the render order. You can change the order in which layers are composed with one another by changing the layer stacking order.

Note: Because of their depth properties, the stacking order of 3D layers in the Timeline panel does not necessarily indicate their spatial position in the composition.

In the Timeline panel, drag the layer names to a new position in the layer stacking order.
To move the selected layers up one level in the layer stacking order, press Ctrl+Alt+Up Arrow (Windows) or Command+Option+Up Arrow (Mac OS); to move the selected layers down one level, press Ctrl+Alt+Down Arrow (Windows) or Command+Option+Down Arrow (Mac OS).
To move the selected layers to the top of the layer stacking order, press Ctrl+Alt+Shift+Up Arrow (Windows) or Command+Option+Shift+Up Arrow (Mac OS); to move the selected layers to the bottom, press Ctrl+Alt+Shift+Down Arrow (Windows) or Command+Option+Shift+Down Arrow (Mac OS).
Choose Layer > Arrange, and then choose Bring Layer Forward, Send Layer Backward, Bring Layer To Front, or Send Layer To Back.

When you copy (or cut) and paste layers, the layers are pasted so that they appear from top to bottom in the Timeline panel in the same order in which they were selected before the copy (or cut) operation. You can Ctrl-click (Windows) or Command-click (Mac OS) layers to select them in any arbitrary order, cut them, and then immediately paste them to reorder the layers in the order in which they were selected.

Jeff Almasol provides a script on his redefinery website with which you can change the stacking order of layers in a composition by sorting according to In point, Out point, selection order, layer name, or random order.