The Metropolitan Museum in Manhattan can't really be said to have anything on display that is not a highlight. However, one of my personal favorite parts of the museum is the Frank Lloyd Wright room, a re-creation of the living room at Northome, formerly of Wayzata, Minnesota. The Met's reassembled room contains some beautiful pieces of Wright-designed furniture, including in ingenious collapsable print table and a pair of chairs that seem to be Wright's update of the Roycroft aesthetic. Recently, the met added an excellent virtual tour of the room to their website.
Northome, of course, was and is considered the last of the great FLW Prairie-style homes, and was unforunately torn down and its rooms disassembled in the 1970s; the Met has the living room. The Northome library is in the collection of the Allentown Art Museum in Pennsylvania, and Northome's Hall, complete with the wonderful windows manufactured by the Temple Art Glass Co. for Wright, is at the Minneapolis Institute for the Arts.
I don't know the whereabouts of any other portions of the home - please email me if you know of any. A later generation of the same Little family who Wright originally built the home for made the ridiculous decision to take down Northome and build something smaller on its lot. May the Gods of art and architecture have mercy on their soul.