Pen and paper is how I do it. I keep track of what I planted the previous year and if it grew well where it was, which helps me draw up the plan for the next year.
A fair amount of experimentation goes into it though—I usually pick a new type of plant to grow each year. Some recent picks were multi-colored carrots, spaghetti squash, and cinnamon basil. But I'm not a hardcore gardener by any means.
I hope your garden turned out well this year!