Clue Trees are a concept from the game Millenium's End, by Charles Ryan. As the author describes them,
A Clue Tree is a table, sort of like a flow chart, that outlines the connections between events, people, and bits of information that the characters may come across. It shoudl hav eat least one route form the beginning of the adventure to the end, preferably two or more, so that the players won't be railroaded into a certain line of thinking or course of action. But never let on that there are multiple routes to success, even after the players successfully wrap things up. Players enjoy the belief that they unearthed the single, all important clue in the only place it could be found.
The approach suggested is that the adventure consists of three pieces: the Real Scoop, the Clue Tree, and the descriptions of individual people, places, and things (including maps, character sheets, illustrations, etc.). The Real Scoop is background on the true situation, but it is in the past. The Clue Tree provides on overarching organizational structure to the adventure as it is ongoing.
The following clue tree is from the sample adventure from the core book of Millenium's End, called "The Thanatos Factor".