I've mentioned before that I think placing clues is the trickiest part of mystery writing. After all, you don't want your clues to be too obvious (no neon signs screaming for the reader to pay attention) and you don't want clues to be so hidden that the reader feels duped.
I recently found several pages on the web that I thought would be helpful references for writers looking for skillful clue planting examples. Agatha Christie was a master of the mystery genre, and these websites uncover ways she placed clues.
The first site is actually a study guide for Christie's And Then There Were None. The guide provides a clue tracker that goes chapter by chapter, illuminating the clues that point to the murderer. Naturally, it's more helpful if you've read the book (which is fantastic, if you haven't). You could do some clue-tracking yourself by picking up any paperback mystery and reading it through with a highlighter and pen--marking the clues/red herrings as you go. It's useful to see how other mystery writers create their puzzles.
The second site is an under-construction Wikipedia article. It's, oddly-enough, marked as a possibility for deletion, as of this blog date (click on the "discussion" tab at the top of the article page.) The designation for deletion appears to be a mistake....all the references in the article were from Christie's actual novels. At any rate, it provides an excellent listing of the plot elements (clues, red herrings, etc.) Christie used. Some of them are: clues hidden in plain sight, missing elements, supposedly unreliable characters, and chance remarks. Books that include these elements are mentioned for our reference.
The third site is a website devoted to Agatha Christie. It also includes a list of plot devices used by Christie to puzzle her readers.