I'm wondering if people who are using complex software aren't making this more complicated than they need to be.
One real problem with computers is that it can be harder to locate a file than if you're using paper.
I'm currently working on a series of stories that will (I hope) come together as a coherent whole (novel) and so far at least it's not at all difficult to just create paper file folders for each story. I have a simple list of who my characters are, what's the deal with each, and just add to it as needed. That's all on one sheet of paper.
Now I'm doing all of my actual typing on a computer, and everything is also saved as a word file.
And I have taken a little time with Writer's Cafe, but as pared down as that apparently is, it still overcomplicates things, in my opinion. Anyway, I have no reason to doubt someone who swears by some sort of writing or organizational software, but I'm still yet to see anything that fits my personal writing style.
But I'm still interested in hearing what others have tried.