For a site’s information wireframe, I do it by hand. I use an index card to represent each HTML page, and pin them up vertically corresponding to the general page hierarchy. On each index card I put the page’s filename and title, followed by a sketch if needed, and a summarized list of the information on the page (including file names of where this info will come from, or referencing an email where the info is contained, etc). I can also list the information I need to get from the client, as well as keep a note on the general progress of the page (waiting for content, needs content inserted, page complete). Links can be represented with colored strings if needed. The cards can stack up easily if they need to be taken somewhere but I’ve never had to do that. Having them stacked also makes it easy to flip through them quickly and compile lists of what needs to be done, or what info to request, etc. Since I rarely work with other designers, and the sites I create are pretty small and don’t require a lot of client consultation for the info design, I don’t need to have a system that’s easy for others to see or access.