Pen and paperA modular approach offers the most flexibility.
The problem is that every book I write I do it differently, and no software is flexible enough to both offer all possible options and be free of clutter. I use a mix of taking notes in paper notebooks, outlining on loose paper and small file cards (with the help of scissors, glue, colored markers and a large floor --– a very sensual and fun process), writing in a text editor (TextWrangler) and writing and rewriting in Scrivener. I have also used Aeon Timeline, Excel, HTML files (edited in an editor and viewed in a browser), photographs, and other applications and media to help me alongside my paper/editor/Scrivener core apps.
If you want a software that exactly fits your personal writing style, you need to program it yourself --– possibly a new one for every new book that you approach differently. The more flexible approach is modular, using different software for the different tasks you need done. This is not a costly approach, since a lot of the software you'll need is either free and open source, or obscenely cheap.