I have been using for a while now an image manipulation program called Gimp. This son of a bitch has been using layers for a while now and I finally grabbed a book about digital photography and gave layers a whirl. I really like how you can take two layers, change one and tweak the opacity to blend them together. Very useful I have found when adjusting the sky in scenic shots. The two pictures below I darkened the sky and adjusted its contrast to bring the clouds out more.
Torch Lake before manipulation
Torch Lake after manipulation
The view from Empire Bluffs before manipulation
The view from Empire Bluffs after manipulation