As usual in the development cycle there are so may tools that can be used.
Paper and Pen/Pencil, for many good designers the way to go. Since I am not a good designer, rather a lazy guy, after all I want to do is go swimming in the ocean and then hang out goofing off, I use paper and pen/pencil lightly. Mainly it seems like a waste of time and messy.
Drawing using a Watcom, now this makes sense, or if you are lucky enough to have a touchscreen system running WIndows XP, Vista, WIndows 7 or WIndows 8 you could use OneNote or the incuded Journal to make your art. That way if you come up with something good then you reuse it. This is the one I am going to use.
Later you might want to use PowerPoint to storyboard your game when you have better drawings and ideas. Right now, I am not using it, but I have seen some students use this process and the result was NUTS! In a good way. So consider using Powerpoint, maybe after you have a good idea of the flow.
Seriously, storyboarding is important to the overall game design, unless you just want to slam code, then just slam code.
In this case I use the free Journal that comes with the Tablets running XP, Vista, Windows 7, Windows 8. The actual graphics are better then the graphics I show below, but you should get the idea, that at this time, it isn’t about perfection (if it is, get someone else to work with you, perfection is a good thing, but not right now).
Ok, here is the initial storyboard: