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One thing Scrivener allows you to do is collect research materials. You can include recordings, articles, video, web pages, pastes of anything, photos -- all sorts of things. You just tuck them into the "Research" area of your Scrivener files for the book.
I also toss the detritus from the cutting-room floor there. Scenes I've cut, ideas I decided in the end not to use -- they all end up in in my Scrivener book file.
One day, if a book I write (or a book by anyone who uses Scrivener) becomes hugely popular, I imagine these source files will be of interest. They might sell for a pretty penny in our money-crazed culture. I could see them being bid on at Southeby's in ten or twenty years.
Even if my files don't become sacred relics, if there is a fan base for my books I plan to release cut scenes on the blog, to give people another taste of a book they enjoyed. I see this as a real bonus. I'd love to read more of a book I thought I'd finished long ago. Extra scenes! Sounds hot.
There are no negatives with Scrivener. It's all gravy. If you haven't tried it, you might want to check it out. And if you're on a PC, hang on. I expect there will be a version for you later this year. It is so easy to write with Scrivener. Just open it up, take a sip of espresso and you're writing. It's really that simple. (Well, okay, it isn't; but when you're ready to write, Scrivener can help.)