You can separate each scene of your novel into a separate file, and organise those files into separate folders (your chapters), all within your manuscript--Scrivener then shows you that structure as a sidebar, so you can very quickly jump around from scene to scene, chapter to chapter. You can rearrange scenes and chapters easily, just by dragging and dropping files in the sidebar. Then when it's time to print or export your document into manuscript or e-pub formats, you can tell it exactly what you want exported, and how you want it to look, without actually changing the document itself. You can quickly override fonts, rich-text features, and layout with whatever font the publisher wants--all without changing the base document itself. And it's set up with excellent pre-set formats for all sorts of writing--novels, screenplays, non-fiction books, essays...
You can also link research documents directly to your manuscript, so that you can quickly click to them as you write--those documents also show up on your sidebar. No more going back to Safari every time you want to check a fact--just link the page to your document, and it's right there for you.
You can create character sketches that also show up in your sidebar for easy reference. There's a place for notes on each chapter. You can create chapter summaries, linked to each chapter, and then print out a synopsis from them. You can switch modes so instead of all the clutter around your writing, all you see is the page (no distractions). There's lots more--I honestly don't even begin to use all the features.
The big thing for me, though, is its stability. In Word, once your document exceeds about 40 pages, or if you have tables or images or odd formatting in it, it becomes incredibly unstable--images and tables will move from one place to another. Formatting will change unexpectedly. Word will crash entirely. Scrivener doesn't have these problems. It was designed to deal with book-length documents.
No, I haven't been paid by Scrivener to rave about the software. I just really like it. I would have given up writing books a long time ago if I had to do it in Word. Scrivener makes it easy.