See http://research.microsoft.com/%7Edongyu/Office2007EqnNumber.txt
for a Office Macro Solution.
A good discussion can be found at http://forums.microsoft.com/TechNet/ShowPost.aspx?PostID=593531&SiteID=17
although the result is “a perfect solution just doesn’t exist”.
See the top 3 icons (counting from right), they are respectively: InsertNumberedEquation, InsertNumberReference, UpdateAllNumbers
