I use two Moleskine journals daily. The smaller, lined journal is called a "Pocket Notebook," and is what I use to stay on top of everything I need be be working on. It is essentially a list of tasks and projects. I have blogged about it before and you can see the basic set-up at Hyaline Skies.
The second is a large, blank Notebook, which I call my workbook. I am still tweaking how it functions, but for the last year I sketched out most of my work and ideas in them, and then created final drafts on the computer. My workbook includes sermon perparation, blog ideas, brainstorming for ministry, etc. For example, the other day Steve and I sat down to work out details for an exciting project we are working on and everything went into the Moleskine. That work follows a couple pages where I sketched out ideas for our Christmas sermon series. I go with blank pages because I often diagram, brainmap, and doodle my thoughts. It also allows for greater freedom in writing across the pages horizonatally or vertically. Steve and I were also recently talking about the workbook idea and the value of numbering the odd pages and creating an index in the front for the more important work that we would want to reference in the future.
This is not for everyone. I am sure many of you remain far more organized with other systems. This is just what works for me.