Russell Blake’s Outlining Method– He uses spreadsheets to plan out his work in detail and has a system for color coding them and keeping the pace up. Rather impressive. This is a hyper-productive author who writes almost a book a month using this method.
The Subway Method of Mapping Out Your Story- This is a technique for visual thinkers to use that would be helpful during the planning stage. Check the comments of the article for lots of links to software to help you with using the technique.
How to Plan a Scene- A nice video on planning scenes, and it comes with an amazing Scene Planner sheet (in PDF and Scrivener Template format)
Worksheets for Writers– Author Jami Gold curates this page that collects worksheets, spreadsheets and templates based on the plotting and planning advice of Blake Synder, Michael Hague and others. (It even has a specific Romance planning Beat Sheet if you want to write a romance novel.)
Scapple– The creators of Scrivener have also created this extremely intuitive mind-mapping software for those of you who are more visual planners. It’s got a free trial, and if you want to take a more visual approach this might help you a lot! (There’s other similar free programs called Freemind and XMind you might check out as well.)
Speaking of Mind Mapping, I’ve found two noteworthy approaches to using mind mapping to plan stories. Paul Donovan Campos‘ method and this one from No Wasted Ink. I should note that most mind-mapping methods are more brainstorming and less about organizing, but the No Wasted Ink approach is a step by step one for putting together a solid book foundation.