I am hoping to find the article that had something to do with mapping dungeons and used the idea of a "lock and key" to create interesting dungeons and adventures.
The author described how it would work in the traditional sense, with a physical key and a physical door, but also applied the concept to adventures in which clues served as locks and keys to solve a mystery.
It was a very good article, but I do not remember the author, title, or issue. I just know it was during 3rd edition. It could have been in either Dungeon or Dragon, and perhaps in some iteration of the Dungeoncraft series, though I'm not sure.
It's a great article, and I wish I knew where I read it. It could have even been an old DM Toolbox, or even something online at WotC.
What I really want to look at is how the author used a flowchart to keep track of his clues in his mystery, treating each clue like a metaphorical "lock and key." I've been trying to do it myself, but nothing quite matches the elegance that I remember from the article.
I realize this is a bit late, but have you read the Locke & Key comic series? The premise centers around an old New England mansion (in the fictional town of Lovecraft, if that helps you imagine it) which contains a series of magical keys, each one granting a different effect when you step through a door after using said key. One key lets the you step through the door to any location you know. Other keys turn you into different things (ghost, giant, animal, etc.). There's many more with different effects. There's a great deal more to the story, and it's a fantastic comic book series, but it may be that some of the ideas contained theirin might help you out.
