In Jason Cordova’s The Between, the Mastermind Clues are not quite mechanical Clues per se, but thematic ticks on a clock that track the arc of a campaign, ending with the facilitator writing a Mastermind Threat.
In play, my players wanted to use the Mastermind Clues in the final Mastermind Threat somehow and so I allowed the hunters to substitute any clues they discovered during the final Threat with one of the Mastermind Clues they uncovered over the course of the campaign arc, if it would better suit their Theory. How have other folks in the community made use of Mastermind Clues in their games, whether drifting the standard rule of play or through highlighting narrative themes?