I'm about 10,000 words into my new work-in-progress, a YA mystery. This is a departure from my usual sci-fi/fantasy bent (although it does have a speculative element, because I really can't help myself), so I found myself at something of a loss when it was time to plot the novel.
1. Dramatic Structure and Plot, by Hallie Ephron for mysterywriters.org
This extremely useful overview of mystery writing gives you some of the basics, like giving your sleuth a hard time and how to write a hook-y opening. The list at the end of cliché endings to avoid is especially helpful.
2. 5 Tips for Plotting a Mystery, by Pamela Fagan Hutchins
The first piece of advice here (start with an end and work toward a beginning) gave me my first aha! moment in my novel plotting. I figured out my climactic scene and the big reveal of whodunit, then worked backward. That made it much easier to flesh out the beginning and middle of the story.
3. Understanding the Essentials of Writing a Murder Mystery, by Bronwyn Hemus
Having read quite a few mysteries, I knew a progression of clues was a must, but I was foggy on how that worked, exactly. This article discusses the importance of feeding the reader clues that aren't obvious, but that could be followed to arrive at the solution to the mystery in retrospect (easier said than done, but at least I know that I should be doing it...)
And, just for fun...
4. Mystery Plot Generator
This mad-libs style blurb generator is perfect when you're stuck on some aspect of your plot and need some comic relief. My favorite part is the automatically generated critics' reviews—brilliant! :-)