I recently read a blog, wherein the author commented on how to design and run a fantasy murder mystery adventure.
If I remember correctly, that blogger noted that the gathering of clues, and the identification of the culprit, depends on the skills of the players and the DM, in addition to the quality of the clues provided. Sometimes, what seems the obvious solution, to the DM, eludes the players, either because the DM failed to provide certain clues (or gave ambiguous clues), or the players assigned higher value to macguffins or peripheral information, and did not pay attention when a particularly critical clue was revealed.
While the players must play an active role in gathering clues, ultimately, the success of a murder mystery adventure relies heavily on the DM. If the DM does not provide the necessary clues, or misdirects the players with macguffins, the players ability to identify the murder will be fatally impaired.
I have always enjoyed running murder mystery adventures, but my DM skills are mediocre at best. As a cheat, in order to compensate for the inevitable misdirections and macguffins which I inadvertently pass on to the players, I tend NOT to prepare one correct solution.
Instead, I come up with several clues, usually 20-30, that point to different suspects. I sprinkle those about, in various locations, and with various NPCs. The characters must gather up the clues, visiting several locations, and talking to different NPCs. As they gather the clues, they will come up with their own solution. If it seems a reasonable solution, based on the clues gathered, I make that the solution.
This may seem like pandering. Perhaps it is. But to me it results in a far more satisfying conclusion to a murder mystery adventure, since the players still do all the leg-work, gathering the clues, and their solution is based on their synthesis of those clues. The alternative, with the players and the DM staring in frustration at each other because a clue was missed or misunderstood, is less palatable to me.
Of course, a better DM will not have to rely on this method.