I haven't heard of anyone being sued, but it's probably happened. For unfinished projects, commonly what happens is there will be a cease and desist letter and then the people doing the fangame get scared and take things down.
As far as I have been able to gauge the social climate regarding asking permission, a rule of thumb might be that the bigger the game company, the more likely they will unilaterally deny requests to use their intellectual property for free, whereas the more Indie the game's production team, the more likely you will experience negative backlash from fans for using their intellectual property without permission.
Take that intuition with a grain of salt, though.
As far as I have been able to gauge the social climate regarding asking permission, a rule of thumb might be that the bigger the game company, the more likely they will unilaterally deny requests to use their intellectual property for free, whereas the more Indie the game's production team, the more likely you will experience negative backlash from fans for using their intellectual property without permission.
Take that intuition with a grain of salt, though.