Mitakihara Town (見滝原町,Mitakihara-chō) is a provincial city where the story takes place. It was not until recently that development began in the town. Much modern architecture has been constructed since.
Also Mitakihara City (見滝原市,Mitakihara-shi) is mentioned in the story. The evacuation notice in Episode 11 refers to Mitakihara City. Mitakihara Town is most likely another name used for Mitakihara City. It is possible the town is a subdivision of the city, though if this were the case, it'd be more likely referred to as a ward.
Several shots of what is thought to be the Empire States Building without its spire. Appears when Kyouko is spying on Sayaka with her magically-enhanced goggles.
A proposed complex of three skyscrapers. In March 2009, the project was cancelled. It appears during the scene with Homura having a conversation with Junko while watching over the city across the river.
The National Art Center, Tokyo (国立新美術館Kokuritsu Shinbijutsukan) is a museum in Roppongi, Minato, Tokyo, Japan. A joint project of the Agency for Cultural Affairs and the National Museums Independent Administrative Institution, it stands on a site formerly occupied by a research facility of the University of Tokyo.
Milan Cathedral (Italian: Duomo di Milano; Lombard: Domm de Milan) is the cathedral church of Milan, Italy. Dedicated to Santa Maria Nascente (Saint Mary Nascent), it is the seat of the Archbishop of Milan, currently Cardinal Angelo Scola. The Gothic cathedral took nearly six centuries to complete. It is the fifth largest cathedral in the world and the largest in the Italian state territory.
Work started on a new Berlin Central Station after the fall of the Berlin Wall, as a symbol of a reunified Germany. The station itself vaguely resembles a mushroom.
An aerial view of Mitakihara City as seen in the Madoka Magica Portable game. It may or may not be an approximation of what the city looks like in the anime.