It may be overkill for most—it’s not the easiest thing to set up and it’s got a high learning curve—but for heavy research and world-building I’ve found Semantic MediaWiki revolutionary.
You can create auto-generated and auto-updating maps, timelines, tables, etc., and make live queries that pull information from all relevant pages. (For instance, if you write pages for a bunch of events and annotate them with dates, locations, and which characters are involved, you can create a map and itinerary for each character and a list of all the characters they’ve met or interacted with. If two characters meet in a particular place, you can generate a list of the most recent events that happened to each character, recent events at that location, past events where both characters were present, people and places they know in common, etc. And if you decide to shuffle events around, everything updates accordingly.) It’s also great for collaborative writing, it can be accessed through the web from any device, and it has automatic versioning. It’s almost insanely powerful, and of course it’s FOSS.