People like TOGAF because it is specific and proscriptive
Good available samples
Layers Conceptual -> Logical -> Physical work well
U Mich pulled out specific best practicss
Tools
MS Office or similar Google Docs, Wikis are what most people use. It is the lowest common denominator.
UBC used Troux (http://www.troux.com/Image Removed) to do an engagement analysis mapping capabilities to technology to show gaps and overlaps. Part of strategic planning