Currently on the worldbuilding/outlining phase.
I’m using a customized self-hosted Semantic MediaWiki installation, and can’t imagine doing it any other way—it’s like Wikipedia with the added ability to aggregate and live-update information from related pages. For instance, I can create a story event page with the place, date, and list of characters involved—and just from that, each character’s page has a map of all the places they’ve been, a timeline of all the events they’ve been present at, and a list of all the characters they’ve met; and it all gets updated whenever I add or edit an event.
Plus it’s on a web server, so I can access it from any device with an internet connection.
The Steerswoman series by Rosemary Kirstein, and the Merchant Princes series by Charles Stross—both series that may not seem like sci-fi at first, but become increasingly so as they progress.