Scrivener is what I use to write my manuscript. From outlining, to note taking, to character sheets, it can do it all. Once you have your book written, you can export it to a variety of formats. You can even set up your own templates, and change the theme of the layout to suit your mood!
Trello is my visual outline in action. It’s drag and drop, easy to organize, and did I mention VISUAL? I throw all my photos of characters, places, and objects in there, as well as things like my running tally of tracks for my novel soundtracks. I also keep things like my important links and my branding info in Trello. It’s even better with Gold!