I use Scrivener for this. I have a separate Project entitled WorldReference. Everything that is Altearth, regardless of the specific story, goes here. It has been invaluable.
OneNote could work. I've heard of people using it. Whatever you use, you really need it to have some sort of hierarchical tools--folders within folders--and to have a search function. The rest is optional icing.
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There is also an alternative to Scrivener called yWriter. It's free, that's why I like it.
Originally Posted by oenanthe
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"The tree that bends to the wind has no broken branches; the eye that sees cannot see itself...unless of course, it's looking in a mirror."
Thank God. I thought I was the only one.
Originally Posted by spectre
I don't use it as much anymore, and it doesn't appear to do even half of what Scrivener does. But it's an excellent free resource.