Story ideas come from all kinds of sources. I use a small Moleskine notebook to jot most of these down. 
On another message board I read a great post that said keeping a notebook was good for creative people because you can only keep so many ideas in your head at one time. So, if you put them in a notebook, you free up space for more. I thought that was brilliant insight into the creative process.
But what’s to be done with these ideas? Well, once I settle in to write a book, I crack open a new, larger sized notebook like this one:
Inside, I write a rambling description of the story that is basically a collection of the embellished ideas from the small Moleskine. I cross reference this first description with the Moleskines so that if I ever want to go back to the original source, I can find it. This gets to be a difficult problem when the story ideas show up in several of the Moleskines. When the general description is finished, I’ll start sketching major scenes, characters, and locations. From these blocks I start building up the story with outlines. Sometimes an outline is unnecessary, especially when the characters are at critical moments. Still, an outline keeps the writing on track and the writer out of trouble. If you don’t know where you’re going in the story, you’re stuck. Some people call this writer’s block and perhaps they’re right. However, with a decent outline, there’s always work to be done.
And that’s how I start a story. Finishing it is another matter. People often ask me if it’s difficult to write a book. My answer is this: It’s easy to start a book. It’s tremendously difficult to finish one. But we’ll talk about that later.

Oh man, I hear EVERYTHING in this post.
I actually started doing table of contents for all my journals, which is a pain in the butt, but if you do it as you go along, it’ll really help later on when you’re cross-referencing.
And I don’t love outlines, but I’ve found, like you said, that having a rough one really helps keep you going through a “block.”
It’s easy to start a book. It’s tremendously difficult to finish one.
HEAR HEAR!