According to an interview with Urobuchi Gen on the brochure of Mahou Shoujo Madoka★Magica Movie 1: Hajimari no Monogatari, the Madoka Magica project will not end with the three movies. However, Urobuchi does not know what the continuation of the project will be like. According to Sports Hochi newspaper, Urobuchi plans a two-cours TV series and he is thinking of inviting a new writer. He said Madoka project must be continued even if he leaves the team.
Sources: Scan of the article, Sports Hochi
Unconfirmed info:
The third movie “Mahou Shoujo Madoka Majica New Chapter: The Tale of Rebellion” (Shinsho: Hangyaku no Monogatari) will be premiered in 2013. The story will take place in a newly reconstructed world.