An annotated outline is an important part of the pre-writing and research process. The annotated outline can help you to see your arguments played out and how different parts of the paper will relate to one another. This helps to make your writing a cohesive whole.
Write the annotated outline only after you have conducted preliminary research. If you begin writing it before you have compiled any research you will not know enough about your topic or the direction of your paper to properly outline. The first step in constructing your annotated outline is typing in one sentence the thesis or purpose of your paper. This is what you are going to argue, or demonstrate to the reader in the course of her reading the paper.
Next, you will outline the paper. Instead of writing keywords as you would in a regular outline, you will write out a description of what you intend to write or argue in a particular paragraph. Include all major arguments and sub-arguments. It also may be helpful to outline what you will use as a transition between one section of your paper and another.
Finally, double check your annotated outline for consistency. Make sure your arguments are well-supported. If there are any holes that need to be filled, now is the time to acquire that additional source material - not when you are halfway through writing the paper. An example of an annotated outline, written for my research paper, "Much to do About Suffering" can be found on the examples page.