I worked as the SM for an Improv troupe, and the way we settled upon calling cues in the midst of games would be simple: One of three people would be the one who could call "Scene." I was one, the Director was another and the Assistant Director was the third. When we felt a scene had accomplished all it could, and we were ending on a high note: Black out called by me to punch the end of the scene or the D/AD would yell "Scene" and then the blackout. So in this instance, it's easier than an experimental piece. I had to have understanding of improv games, situations, and timing in order to end a scene with the right momentum and I had to be quick on my feet to make the other calls. There is nothing worse than calling a blackout when an improver is still moving forward with the scene and you make a bad call to end the game early. It leaves everyone feeling unsatisfied.
I preached this in a thread elsewhere on this forum saying you need to memorize as much as you can leading into a tech. I'd say the same kind of principle would apply here. If the piece is generally supposed to cover the same information, but isn't tied to a script then memorize the general patterns the cast might take. Maybe there's one actor who does the same thing at the same moment in the progression of the show: Take a cue off that. There may not be a script, but there may very well be patterns you can cue off of.
Same goes for a script being created by an exploration process. If there's a lot of chaos on stage, find the one thing you want to cue off of: Key word, phrase, movement etc.
And I have completely lost my train of thought so I'm going to try to stop rooting around in my brain trying to figure out what else I mean to say.