For my story writing, I use a combination of Scrivener and WriteMonkey. Scrivener is used more for organizational and planning purposes - it allows you to break up the story by scenes and organize them as cards, as well as track characters, settings, and other things. I actually don't do much of my writing in Scrivener; I just use it to track the different pieces. It would be a little excessive for just a short story, but for anything longer than a few pages, it really helps. It's not free, but it goes on sale quite often, and you can get a student discount as well, so it's possible to get it for pretty cheap.
WriteMonkey is very similar to FocusWriter. I actually really like FocusWriter, too, and used that before WriteMonkey. However, FocusWriter had some troubles for me on Windows 8 for some reason, and WriteMonkey has a few extra features I really like. I find its word counter to be a little more in my style than FocusWriter, and the ability to focus in on a single paragraph and dim all the rest is really cool and helps keep me focused. At the core, they're pretty similar, though, so it's more of a matter of what works best of your system and which you prefer. Like FocusWriter, it's free with the option for a donation.
For really complicated stories, I also throw Aeon Timeline into the mix, which syncs with Scrivener, and allows you to have a visual view of character relationships over the course of the story, timeline of events split by plot threads and sub threads, and character development throughout the story as well. I'm actually just trying this one out, but so far, I really love it. My only complaint is that sometimes all of the organizing can start to take time away from the actual writing.