I have a general idea of the story I want to do. I use Celtx to write the outline and I do script some parts of the story. I never end up sticking to my script, however, as I'm frequently thinking up other ways of telling the next part of the story. Sometimes that's a good thing, sometimes not. I think if the story is quite complex, then scripting, to some extent, is a good idea.
My animated films, on the other hand, were all made up as I went along. You have a lot of time to think while animating