I write short fiction, mostly S-F and horror. Lately I've tried several demos of writing software such as Writer's Software Companion, StoryBuilder, StoryCraft and Fiction Magic. Roxianne Moore's article in Suite101 was the first really helpful info I've come across. I've never tried a novel, and the idea boggles my mind.
Short stories are hard enough.
I sell my stories but feel I could do better as I'm self-taught in fiction. Many programs are definitely geared toward writing novels, but they can also be adapted for short stories. Writer's Software Companion places less emphasis on fitting your story into a specific structure and more on the mechanics of good storytelling. So, in that regard, it can be used by writers of short works or novels. You may decide to ignore some sections that don't pertain to your medium, but they'll be there if you decide to tackle a longer story.