We're working on improving our site-mapping phase of our web projects here at Cosmic. Our approach here is inspired by Angie and her project here and Charlie and the guys at Focus Lab.
Although it adds a little upfront work before wireframing, it really helps to think through the entire architecture and get it in ink for reference throughout the project.
I'm interested to hear how some of you handle this stage in the process. Although we're fast in illustrator, it seems like there might be a better tool for the job?