You can target a layer to apply an appearance by clicking on the circle to the right of its name in the Appearance palette.

This is not possible, however, if the layer is empty.

This is also not possible if the only thing the layer contains is empty layers.

This is also not possible if all the children of the layer are locked. Or invisible.

There must be at least one unlocked, visible non-layer object in a layer before you can target it.

I am most often annoyed by trying and failing to target a layer with a bunch of locked child layers in it, but I would like to see all of these restrictions lifted, so that it's much easier to apply effects to nested layer structures.