Tipped from Flojin, I've been using Scrivener to write cookbooks from here. I have looots of random pages, recipes, research and files floating around so this has helped me endlessly to organize my thoughts.
It's like a whole operating system, with tons of features for creating an customizable organization system. You can store any kind of web-based research including web pages, pdfs, sounds, images, etc.
I love the interface: you can see your folders and subfolders, assign all kinds of metadata tags and sort/search it all. There are tons of ways to view your stuff including on corkboards & filecards or lists and folders or icons. It's pretty neat.
I like writing in it too: there's a Composition window that minimizes the background stuff.
In general I hate writing drafts in Microsoft word, though the most recent edition is vastly improved. With Scrivener you can do a very detailed exporting of your draft into a bunch of formats including Word and EPub.