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OneNote can contain everything: background information, audio recording, whole web pages and files. Scrivener is great for outlining but I can never be bothered to fill in the Synopsis cards, prefering to make notes in the Document Notes area of the Inspector - notes about things which need to be done to the scene etc.
If we're talking fiction, I've fallen in love with a new program called The Novel Factory. I've found this really useful for guiding the structure of a book. While using the trial (which is only seven days) I took one of the chapters from my WIP and worked it using the program; the "chapter" could now stand as the basis for a novel in itself and will need to be considerably pared down to slot into the original WIP.
Different software tends to be great at different things. I still like Word for basic outlining (using the Outline View).
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