What I Use
Scrivener - A useful tool for formatting and compiling, as well as an organizational tool for the initial writing process. Having grown up in the era of notebooks and, at best, Word Perfect (who remembers that eyeblinding blue screen?) I prefer to use a simple word processor for most of my computer writing, but eventually it goes into Scrivener.
Aeon Timeline - Now in its second version, a useful tool for keeping events from running into each other. Can also export various timelines into other format, allows for longer notes than the regular timeline display shows, etc.
Campaign Cartographer - Useful for those who are comfortable using CAD technology, a map-making program with a variety of features for mapping original territories and worlds.
Write or Die - The stick side of motivating myself to write.
Written? Kitten! - The carrot side of motivating myself to write.
Study and Research Tools
Khan Academy - A good site with many of the basics of math, science, history. If you want to go back to primary school and relearn some of the things you forgot, or if you just want to watch a lecture video a few times a week to enhance your brain, this is a good place for you. Also has some coding classes!
EdX - A wide variety and sizeable number of courses from universities around the world. Quality is generally good but the teaching style varies considerably, so one class might work for you and another class might require the same number of course hours but be done in such a way as to take twice as long. Caveat Discipulus. You can audit classes as well as pay for a certificate.
Coursera - I have not yet actually tried Coursera. A short review will be forthcoming as soon as I do.
JStor - My single biggest reason for wishing I was back in college. A YUGE repository of journals, primary sources, and now books. You can get a pass to read and download a limited number of articles if you have the money for it, otherwise you need to be lucky enough to have a nearby library with access. I whimper in longing.