You'll find this technique especially useful if you're writing something that follows a non-sequential chronology.
Jen talks commercial solutions
If you use Final Draft to write your screenplays, it has a great built-in tool to help you visualize your script in shorthand. It's called the "Script Navigator" in Version 5, and looks like (surprise!) a series of index cards. You can print out the cards if you like the more hands-on approach like me, or view them in a browser window. Go to any scene you want by double-clicking on the card. The Navigator stays open in another window.
You can also use the Navigator to move whole scenes easily and with - well, less chance of deleting an entire section of the script accidentally. Not that I EVER do that.
My best friend in computer world: the CONTROL-Z undo function.
To live a creative life, we must lose our fear of being wrong.
Jen gets more graphic
Another thing I often do, something that helps make sure that the scenes I'm developing actually serve the greater arc of the story, is to actually plot the story on a graph.
I plot the events in chronological order on the X-axis against their emotional impact or significance on the Y-axis. The higher the point, the greater the stakes.
This way, I can start by putting my climactic event on the Y at the highest point I intend to reach, and somewhere about 4/5 of the way along the way - or a little farther when I'm writing for film and I know that there's going to be very little in the way of aftermath.
It's kind of fun to play connect the dots with my outline! Not always the way I approach the complex weaving that goes on when constructing an intricate plot, but a great tool.
Of course, you will develop your own methods, through trial and error, and by investigating your own personal preferences. The way you learn to deal with your problems is part of your development as a writer.