This is only for long stories, my short stories are more or less improvised or experimental (though some use 3 acts structure).
After having a basic concept I create the characters and start developing the plot and characters together. I start taking notes, I write everything that comes to mind, ideas, dialogues, scenes, visual actions or elements, etc., most of which will not make it into the story. When I know more or less what the whole thing will be, what's the major themes, how it begins, what's the middle, how it ends, how it affect or transform the characters, and such, I chose a structure that fits, divide the story into acts and begin writing a full outline. I revise the outline and change what I feel is not working or could be improved. Then I divide the outline into pages, so I know what's happening in each page of the comic (sometimes this change while writing the script if it turns out the material needs more space than I assigned). And, finally, I begin writing the script.
As for characters I have a questionnaire I fill. There are some lists of never ending questions floating around the web, I find them completely unnecessary (though it never hurts to know your characters better) and missing very important points, so here's a list that works great for me. I compiled some of these points from articles in ScriptShadow.net, and added a few things here and there with time (it's still a work in progress), hope you find it useful:
Name:
Date and place of birth:
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Entry: This reminds me I have to introduce the character in a way that is interesting, it's easy to forget even though it should be ovious, so I have it first on my list.
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Description: I only use this for prose, not comics, to remind me to describe the character in an interesting way. For comics I don't use interesting description, but very plain and simple to understand so the artists I work with know exactly what it is I would like them to do.
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Action that defines the character: Early in the story (later too, of course) it's important to use actions to show what your character is about, what's his/her essence.
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Fatal flaw: Your protagonists and antagonists benefit from having one.
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Plot objective: What does your character need to do in this story?
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Life's objective: What's your character's life goals and dreams? (this may not be told in the story, but it will shape your character's behavior and help you write him/her better, especially if the plot gets in the way of your character achieving what they want in life).
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Plot motivation: Why is your character doing what he/she's doing in this story? You better have a good reason.
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Personality: What's your character like?
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Speech notes: How does this character talks like that makes him/her different from your other characters? Your characters better have a voice of their own.
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Details, clothing, compulsions, odd behavior, unique traits, etc.: You don't need to fill them all, or any at all, just if there's something unique about your character that doesn't belong anywhere in the list, you write it here.
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Secrets: If your character hides something from other characters (but not the reader) you have dramatic irony, if your character hides something from the reader you create suspense. Both irony and suspense are strong tools in storytelling, use them!
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Notes: Anything else not covered by this list? Write it here.
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Backstory: Bio of your character, very important to know him/her better, and thus, make a better job writing. This will rarely make it into the story, but it's fundamental if you want a well crafted character.
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Backstory in relation to other characters: If there's been story (and especially conflict) in the past between two characters, it will make their interactions so much fun to write and read. This is perfect to fill your story with dramatic irony.
You may find the order is a little odd, it could be improved moving a few things around, I'm sorry about this, I didn't write this list with the purpose of making it public, so I never cared to make it more presentable.