I've done a few different things in the past, depending on what it is I wanted to accomplish.
1. 3x5 cards. I write a two-sentence summary of every scene in the book, one scene per card. The first sentence is the ACTION, while the second sentence is the emotional/character progress or whatever you want to call it. (Example: "Judy jumps out the window and breaks her leg. Judy thinks Joe won't love her anymore.") I then lay them all out on the floor and see how things look visually. Where's the climax? Do the points flow together or feel disjointed? Is there anything I can take out? Anything missing? I do this for every book, usually several different times at different points in the process. It helps when I've hit a mental wall.
2. Papers tacked to the wall. This is what happens when I have two competing versions of a story and I need to resolve them. (IE, I wrote 10K and then REwrote the same 10K, changing plot elements, but then I discover there are a lot of things about the first version I like better and want to incorporate.) I tack both versions next to each other on the wall, cutting up as necessary for chronological continuity, and then I start highlighting and crossing out things. In my experience, this is pretty crazy-making and didn't really get me anywhere.
3. Print out entire manuscript and rearrange on floor. For my current WIP, I wrote the whole first draft with no chapter breaks - just straight through. So I had to go back and make chapters. So I laid everything out on the living room carpet so I could see how big each chapter was compared to all the others, where the natural breaks were, etc. This worked quite well.
4. Printed out entire manuscript and put in three-ring binder. This was so I could take parts out, mark on them, put them back, etc. It's sitting on a shelf, never opened. Actually this is not the fault of the format - it was too early to do that sort of edit.
5. Printed out entire manuscript, had it bound BACKWARDS at Kinkos. (So that when you open the first page, page 1 is on the left, and the facing page is blank.) This was for my last WIP, and the intent was to make all the notes of changes on the right-hand blank pages. Actually it worked well.
If I think of anything else I will post.