The Name Of The Rose: Three Dimensional Labyrinths

The Name Of The Rose is one of my favorite films. Besides starring Sean Connery and Christian Slater, two fine, accomplished actors, it is set in the 14th century, at a medieval abbey gripped with fear due to a handsome monk's recent and unholy murder. More murders follow. Connery and Slater's characters arrive at the abbey shortly after the first murder, and attempt to solve the crimes. The abbey is the site of a massive library, off-limits to visitors: its contents hold the key to revealing the motive behind the mysterious deaths.
If you have never seen this movie, or have not seen it in some time, you are strongly encouraged to do so. As inspiration for a murder-mystery adventure for fantasy role-playing, this movie has few peers. There is little in the way of combat, but if you like atmosphere, fantastic sets and elaborate puzzles, this is sure to appeal to you.

One of the set-pieces of this film: a labyrinthine library, filled with octagonal rooms and rising and decending staircases. The two principles become separated and lost within the library, and use their wits to locate each other, retrace their steps and eventually find egress. It's commonly held that dungeon labyrinths are a bore, when it comes to rpg adventuring. I'm sympathetic to that view. Imagine your typical dungeon labyrinth, but now in three dimensions. Doesn't seem that appealing, does it? But, instead of being a labyrinth, what if that many-staired and chambered space was rather a nexus-point, a convergence of stairs and passages, going up, down and across, and giving the players a plethora of adventuring alternatives?
That has been on my mind the last couple of days, as I search for a way to design and develop a dungeon environment which provides maximum latitude to the players to strike out and pursue their own dungeon-delving interests. One of the constraints on the full enjoyment of a campaign by role players is the suspicion that they are being railroaded. What could be more freeing, for both the DM and the players, than that the mega-dungeon have a nexus-point, leading to a myriad potential adventures, with easy access to the surface and the dungeon-locales which most interest the players?