I've just started doing this for some screenplays I'm working on, because they're too big for me to trust my feeble mind to keep track of. All I'm really doing though is writing down what I already do in my head.
First, I come up with an idea. Then I come up with a way to expand the idea into an actual story - where it starts, how it ends, and a rough idea of what goes on in between.
Then take three sheets of paper. At the top of each one write ACT I, ACT II or ACT III. Even if these "acts" won't be noticeable in the finished story, it helps give the thing structure. If it's a big story, it may help to list the characters and plot their arc across the pages as well.
Then, I just start filling things in. I may have three or four scenes, events or even just lines of dialogue that I want to use, and it's now that I figure out where they fit in. I know the start and end points, so it's just a question of plotting the course from A to Z. Each of the acts should end with some sort of mini-climax or cliffhanger, with the final act tying everything up (or not, depending on your style wink )
This way, you can see the "shape" of the story. Is the opening third weighed down by too much going on? Is there a huge void in the middle where nothing happens? Are there any characters who outlive their usefulness - and if so, can their actions be taken over by someone else?
Stuff like that. I've found that writing it down really forces me to think about the overall structure, rather than just the "money shots" that I've already thought of.
Then, of course, I just need to write the bloody thing...