Okay, I admit I have a bit of a color coding obsession...maybe a lot of one. I color code my planner (which makes it highly effective, thank-you-very-much), I color code my folders and notebooks to coordinate with the textbook for the class, I color code my notes (which makes for easier and more effective studying), but most of all I color code my scripts. Now, if you've never worked as a stage manager you might not understand the need for such a thing, but I can assure you, it makes my job worlds easier.
Color coding scripts is not only effective for calling the show, it's a great tool for making all of those lists that the directors will ask for at some point in the show. I'm sure other stage managers have their own system for marking scripts, this is just the one I've devised based on the shows I've managed and the needs for those shows (as well as the colors of highlighters/pens/colored pencils/papers/dividers that I could coordinate because when I color code things I want it to all be matchy-matchy).
The standard color system I use is simple:
scenery - green
lights - yellow
sound - blue
costume - pink
props - purple
For some shows you will find that there are more elements to code. For example, when I work a musical, I opt to mark "sounds" in one color and "music" in another. This is helpful in calling the show because there is often one person running the sound effects while another is running the music or directing the orchestra. For one of our shows the playwright (who was working in conjunction with our theatre company) called for several projections to be played behind the action of the play. The projections had to be created and incorporated into the cues of the show. Another show had several different flies that had to be orchestrated into the cues. Another show made use of a fog machine several times throughout the action and I dubbed this as "effects" and also gave it a specified color.
music - dark blue
flies - red
effects- dark green
Each one of the five main sections listed has it's own divider in my prompt book and I keep all of my lists and notes in the appropriate section. I also print my lists on coordinating colors of paper which makes it much easier to help directors find that piece of paper they "never got". (Director: Where's the props list I asked you for last week. Me: I brought it to your office last week. Director: No, I'm sure I never got it. Me: It's purple. Director: Oh, here it is. Thanks.) The optional sections aren't part of the standard prompt book development and don't have a standard divider, but I do include them. sometimes I can't color coordinate the dividers as well but the cues are marked according to the colors listed above. [Side note: there is a prompt book post in the works.]
Recently I found the "Retractable Highlighter" pack (the ones with the funky tribal tattoo designs) that had not only the illusive purple highlighter, but also an unheard of red highlighter. The pack was pretty cheap (woot) and being retractable I don't have to worry about loosing the lids (woot woot). I found a similar set on Amazon in case you're looking for some. The pens I use are flair felt tips that can be found most anywhere, but here's the package I have from Amazon. I also use a brown and a grey flair pen, and those I ordered from Staples.