Scriptwriting software can be of great assistance when writing a graphic novel, as it allows you to easily follow widely-accepted script formats which will make your writing seem more straightforward and professional. Two commonly used programs for this are Final Draft (retailing around $180 as of March 2011) and Movie Magic Screenwriter (retailing around $160 as of March 2011). While both these programs will help you format your script correctly, they're no substitute for carefully planning your story first.
While writing graphic novels may seem quite straightforward, there's actually a wealth of technical information which can assist you in correctly describing what sort of pictures you'd like your artist to create. There are several books which can help you with this, including "Understanding Comics" by Scott Mccloud, a popular favorite and a good introduction for new writers.
Although everybody will have a slightly different process for creating ideas and constructing stories, several programs exist which can help you keep track of different characters and story lines. Two free programs which are particularly useful are Storybook and Freemind. Storybook is specially designed to help you keep track of character locations and interactions, whereas Freemind allows you to create a mind-map of your ideas in order to expand them further.
One of the most important tools at your disposal is other people and what advice and feedback they're able to provide you. There are plenty of websites which will allow you to interact with artists and other graphic novel writers, which can be incredibly useful for getting past difficult problems and eventually finding an artist to collaborate with on the finished product.