GIMP Layers Tutorial
Preamble
If you've ended up here, I assume you are a novice with the GIMP and image manipulation programs generally. Everyone has to start somewhere, so why not here 
I found that when I was learning to use GIMP, with no previous image manipulation experience, the eureka moment was when I understood what layers were and how one could have an effect on another. Once I'd grasped that, the rest just fell into place through experimentation. I hope the following tutorial does the same for you.
This tutorial has been updated for use with GIMP 2.6.
The basics
Having opened the GIMP for the first time you were probably presented with a few boxes (dialogues), of which you recognised maybe one or two (if any!). Do not despair and don't give up, just follow these instructions. Close all the boxes except for the main
GIMP toolbox and the active image window.
Next open the
Layers Dialogue, which can be found in the active image as followsWindows » Dockable Dialogs » Layers
Arrange the main
GIMP toolbox and the Layers Dialogue so that they are to one side of the screen, which gives you most of the desktop for your active image window.A four layer example
The example below on the left shows an image comprising four layers. The image on the right shows the
Layers Dialogue with all the layers that make up the image.
The second set of images show the same layers, with layer 3 brought up to the foreground. This is achieved by selecting layer 3 (the
green layer) in the Layers Dialogue and then clicking the Up button to bring the layer to the top of the stack.
Note:
The layers have had some opacity added to them to make the example easier to understand, don't worry about what this is or how to do it yet, it's explained later.
Layers tutorial
Creating layers
The first thing I'll show you is an image that has two layers. If you want to create one to experiment with as this progresses follow these instructions. In the active image go to
File » New
This creates a new blank image.
Adjust the image to a reasonable size (200×200px) and click
OK.
Duplicating the layer
You now have a 200×200px white image (white, assuming you opted for the default background colour). If you now look at the
Layers Dialogue you will see this image is called Background.
Now go to the
Duplicate Layer button in the Layers Dialogue and click for a duplicated layer, this will beBackground copy.
Choosing a layer colour
With the
Background copy layer selected (highlighted) in the Layers Dialogue, go to the GIMP toolbox and double click on the Foreground Color button, which will open the Change Foreground Color tool.In the
HTML notation box type in FF0000 (this is the hexidecimal code for red) and then click OK.
Adding colour to the layers
In the active image window go to
Edit » Fill with FG Color
This will fill the
Background copy layer with red.In the
Layers Dialogue click on the Background layer to select it.
Repeat the above process with the
Background layer, making this layer blue or hexidecimal code 0000FF.
And then fill the
Background layer with blue.
Ok that's the work over, the rest of this tutorial will just involve tweaking the two layers you have hopefully just created.
Layer order
When you look at the
Layers Dialogue you can see the red & blue layers. The red layer is at the top of the stack, so that is the one that shows up in the image.
It goes up, it goes down
With the blue layer selected in the
Layers Dialogue click the Up arrow. You will now see that the blue layer is at the top of the stack and consequently the image is blue.
Clicking the
Down arrow in the Layers Dialogue will, as I'm sure you have gathered, move the blue layer back to the bottom of the stack.
Ok, all very interesting, but not very useful eh? Well you should now have a clear idea of what a layer actually is. And you will need to know that to start using the GIMP.
Opacity
Ok, it's back to your art classes at school now. If you mix red and blue what colour do you get? And you all answered purple I'm sure
So with our red & blue layers this is very easy to do. Select the top layer in the
Layers Dialogue, for this exercise it doesn't matter if the top layer is the red or the blue.
Now adjust the
Opacity slider in the Layers Dialogue, until it is at 50%. As you will see the image has now turned purple. So now you have used one layer to have an effect on the overall image.
Opacity is not transparency! Opacity is in fact the polar opposite, it achieves the same thing though. Initially your layer will have 100% opacity. If you slide the
Opacity down to 0% the layer would be 100% transparent. Glad we've got that sorted 
