I've looked at many of these aids for writers, including Ulysses and Copywrite, Power Structure. I've tried to tame outliners like Hog Bay and Omni. Each of these has been very close to being helpful, but each has some drawback.

The notes area that Ulysses and Copywrite provide is great, but they don't provide any kind of outlining. Power Structure, does, but it doesn't let you attach notes directly to a particular scene.

So far, and I'm still typing with my fingers crossed, Miss L seems to be filling the bill. The tracking feature for plots and "factors" is fun to watch (it tracks automatically) and useful--you can look at list of plotlines and scenes that belong to them! You can see every time that important gun appears in the story.

The outlining feature is a little awkward, since it's all done via the index card metaphor, but it works. I just discovered you can have sub-decks within a deck, so it really is an outliner, and you can see the full outline in the explorer view.

Very attractive, very useful software.