Gliffy.com is a website that lets you make all sorts of charts and things. I've been using it for a storyline flow chart. It has a lot of functions and it's really helped me out so far. The drawback is that it's a pay service, but you can sign up for a 30 day free trial.
You don't have to make flow charts. It can virtually any kind of chart. You can use it for maps even. I highly suggest other CYS writers to check it out if you need a little visual management for your stories. :)