With the 2007 release of SharePoint and OneNote, Microsoft delivered opportunities for integrating the two. This article reviews what's possible, and puts some structure around the decision.
"I admit upfront to being a bit hesitant about advocating the use of both, for one main reason: If you have one place to look for the current health and status of a team project, each person has a high degree of certainty that they are in sync with everyone else. But once there are two places, or more, there is a higher degree of uncertainty, a greater nagging sense of "What am I missing?" And the freeform nature of OneNote makes me particularly concerned, because ideas, actions, notes and documents of importance can be scattered throughout a notebook -- perfectly within the context of where they should be -- but unless everyone uses OneNote in a common and agreed manner, everyone is going to be potentially confused."
Read the article online, at Michael's blog.