I use Scrivener. It’s not perfect, but it’s the best fit I’ve found for my process. The ability to drag scenes and chapters around and to visualize the emerging manuscript in different ways is invaluable during development.
Much of its functionality could be handled with plain old files and folders, but that gets increasingly difficult for longer projects. Scrivener just gets more helpful as the project grows.
Of particular note is the ability to compile into different formats. I use this for manuscript printing and for digital (Kindle) preparation. For book printing, I use Scribus for layout, but that’s a topic for another day.
Within Scrivener, I keep a folder called Research with subfolders for topics that come up in the books. For the current project, I have folders for Communications, Starvation, Orbital Dynamics, Food, and Space Weapons. In those folders are links and documents and quotes.
I also keep a folder called Notes and a folder called UnusedFragments. More on those later.