Only the GIMP, Pixia and Photoshop support layers, and none save layered png files, that I know of. Actually, I didn't know the format supported that.
Yes, it also can store the hotspots you create and sliced images if the software supports that. For those not knowing what they are, hotspots are regions in an image where you can attach a link to and sliced images are a way to cut one big image into several smaller ones, which for webdesign is a great thing.
