I used Microsoft Binder for a while to organize my documents. It was a little unwieldy since each item was actually a discrete Word doc. Johnn Four at Roleplayingtips likes Milenix MyInfo. I have Microsoft OneNote, which I keep meaning to explore, but I haven't gotten around to it.
There are also quite a few people who use a wiki for that kind of thing. Obsidian Portal is a popular choice for worldbuilding and roleplaying games.