The 'standard' system that has been used at the summer company I'm at right now is to use semi-transparent multi-colored post-it flags for cues.
Let me preface first -- we are an operetta company, so we work out of librettos. During rehearsals we take notes by writing a small number over the measure (or next to the word) where something happens, and write the corresponding action on the blank page opposite (with the number leading it off).
This then leaves the score almost entirely clean for our post-it cues. Since we mostly work out of a score, the post-it flags are great, they span just about the height of a system (one line of music on the page) and because they are semi-translucent, you can still see the music underneath.
For sections of straight dialogue containing cues (no music underscoring), we cut little slivers of the post-it flags and stick them over the cue word (or even as specific as syllable).
And the best part is that the pack comes in five colors -- so for our system we have one for lights, one for spots, one for sound, one for rail, one for cue lights. This way, we can easily look ahead to find the next rail cue -- it will be the next green flag.
But the best part is that we get to have only one copy of the score. Scores are big (and bigger when they are only single-sided), and the idea of having more than one is awful. Unless ABSOLUTELY necessary, I would prefer to have everything in one place.