Maybe I shouldn't admit this, but I don't really do flow charts very often. This is usually something that either the client works up internally as part of their planning phase, or someone else involved in the project does them. I also think to a certain degree they aren't as necessary as they used to be. Most website these days are highly modular, dynamic, flexible and aren't constricted by the apparent structure. Page and entire sections can be reordered on the fly, sometimes even with the administrative tool-set.

Here's one I did recently and I thought it came out really well. I used MS Visio which is part of the fancier versions of Office. I'd never really worked with it before, but I actually has a pretty good time making this up.