I'm actually at the point now where I want to take hundreds of scrappy scenes and bits and pieces and try to give my novel some structure. So the question you've asked is actually uppermost in my mind.
So I like Scrivener. I use it for all my drafting. But it doesn't quite cut it for the big-picture structure stuff, I'm finding.
When I tried to use Scrivener's 'corkboard' view, which lets you see all your little pieces of novel as pseudo-index cards on a pseudo corkboard, I found it impossible to manage because there were simply too many. Maybe if I had several enormous monitors rather than a single 15" laptop, it would work better. But it just didn't work for me.
What I'm finding works much better is not software at all, but the very thing Scrivener is trying to emulate: a large corkboard and a big stack of small index cards. I'm talking physical objects here - call me a Luddite. Rearranging and grouping the scenes is easier and more satisfying because I can see everything at once. If I run out of room I can just buy another corkboard - they're only about twenty bucks at Target.
Of course, there will be some additional work to apply what I come up with, structurally, onto my digital manuscript. But I think it's worthwhile. Convenience is overrated.