I first use paper and pencil, but then I transcribe and keep it up to date electronically. http://lucidchart.com has been my favorite service as it is free for simpler projects and can be upgraded if you need more complexity. I've watched the project grow from an idea, to recruiting developers in my CS classes, to a full blown project which has exceeded my expectations. It's exciting to watch!
Re: Ask HN: What software for diagrams and flowcharts do you use?
#11Seconding Lucid Chart. It's great.