This museum houses the unique history of the city.
It is multi-leveled, so don't think that the primary level with the special exhibit is the end of the road -- press forward if you don't find the exhibit interesting and hit the treasure troves upstairs.
This museum's highlights include two full scale models of Vienna; one prior to the great rennovations under Wilhelm and one after (the Hapsburg leaders decided to tear down the wall around the city and commisioned the great architects of the day to build a series of marvelous civic buildings in its place including the Parliament, Art History and Natural History Museums).
Also featured, and not to be missed, is a full display of Turkish battle armour and weapons from the two great sieges of Vienna (both of which Vienna successfully turned back).
Web site:
http://www.museum.vienna.at/dynamicPage.asp?MenuID=1687