Most of the stories I've written have come from having either a particular character concept or having a particular "scene" I want to write about.
Although I'm a great one for writing lists etc, I really don't plan out my stories on paper. I find once I get to writing, I tend to deviate a lot and will often write massive spontaneous sections much better than anything I planned.
For example, I once wrote a story purely for the sake of a female character I'd thought of and yet throughout the course of writing I ended up becoming more interested with the other characters, who were effectively footnotes in the beginning stages.
That said, I don't necessarily think this the perfect way to write- when Ian McEwan wrote that godawful Enduring Love book, he claimed to have started writing a scene which is actually near the end of the book, based on a random idea he had about some guy obtaining a gun, without knowing anything else about the story. When I actually read the book, I found this "starting scene" completely irrelevant and out of place in the story and it stuck out like a sore thumb.
I remember being told by a teacher once that everybody writes a story in a different way and you shouldn't really be too worried about criticisms of your creative process as long as you keep perspective on the whole story throughout.