This is going to be heavy on pictures, light on text. I use yWriter, which I've mentioned before. I recently downloaded Scrivener for windows, and while it's interface is dead on sexy, it seems to lack some of the features that yWriter has.
As part of a discussion on twitter today, I decided to do some screen captures showing how yWriter handles the metadata of a scene: which POV is it, which characters are present, where it takes place, how long the scene lasts in-story, etc. All of this is compiled into reports that will let you see (for example) which of your characters is getting the most screen-time, what items are important and which are just MacGuffins, the pacing and tension balancing of your scenes within the whole story arc, etc.
I don't use all of these features, and you can similarly ignore the ones you don't need. It's nice to be able to keep my characters straight, though, and to have changes I make in one place propagate throughout the manuscript.
Each photo below is a different screen tab for Chapter 2, Scene 3 of "Goodbye Grammarian". Click to enlarge.
===== Feel free to comment on this or any other post.