I don't use it myself, but from what other authors I know have said, Scrivener is the gold standard for writer's tools. I think novelists in particular love it, but I hear it's pretty nice for short stories too.
As for me, my main tool is Google Docs. I've got all my current open drafts organized in one folder, and other folders for finished drafts on submission, sold stories, and one where I keep drafts specially formatted for Year's Best anthology submissions, after they sell. And I have a folder for trunked stories, that occasionally get resurrected or cannibalized.
I also have an all-purpose archive folder for when I back up a draft before major revisions. To date, I've never ever pulled anything out of that archive, but it settles down the itchy part of my brain that's afraid I'm gonna botch a revision and somehow make it worse than the first draft.
I like Google Docs for a couple reasons: it has all the basic functionality of Word, easily allows me to export in different formats (.rtf, .docx, etc), and (perhaps most importantly!) it auto-saves as I type. I also like that I can access it from any device/computer with internet, so it's not all tied to one physical terminal.
One feature I personally wish Google Docs had was an easy way for a not-programmer like myself to convert between formats quickly. Some markets want me to change all italics to underlines, or to _underscores_, and so forth. There's really only a handful of variations, but they're annoying to do by hand, especially if you're me and you write a lot of stories. So in my wildest dreams, there would be a way to set up several basic formats, and just download/email a draft in the one needed.
I don't really know about outlines and character sheets--once again, maybe for novelists? I'm not writing a novel right now, so hard for me to speak to that.