You can use Core Image Filters in Opacity to add interesting effects to your images. Filters appear in your image as a special type of layer. Every other layer that is "lower" in the layer order has the filter applied to it. If you want to limit the layers that a filter affects, you can put the filter layer with the layers you want in a folder layer-then only the layers in the folder will be affected by the filter.
You can also use a filter layer's mask to limit what areas of the image the filter affects.
Mac OS X includes a large number of filters that you can use with Opacity. You can also use install third party filters and use them the same way.