Complex Network Design Tools?

I'm-Not-A-BOFH asks: "How do you do your large scale network design? I am currently designing a large enterprise network - and there is a ton of information to track and think about. I use AutoCAD, Visio and Cisco Configmaker (which sucks) and many other applications. I am looking for software specifically designed to help you design a network. What tools do you use - and what tools are out there that maybe are little known? How do you begin to manage network documentation when your hosts get into the thousands and your routers and routes into the hundreds? I am really just interested in the tools used to accomplish this - as all the tools I have been finding are just not adequate or well thought out. Please let me know what you think is invaluable to you when you design your systems."