Witch Hunter Robin, Koukaku Kidoutai: Stand Alone Complex Recommendations
Both series focus on a group of people within an organizations that perform special tasks; Section 9 is to GitS as STNJ is to WHR. They both contain lots of philosophizing and the stories become very very similar it around half way.
Both shows are very similar in the way they are arranged. Ghost in the Shell has both stand alone and complex episodes nearly all the way through, and Witch Hunter Robin starts with unrelated 'stand alone' episodes before getting into the actual 'complex' story. Both anime are fairly dark and mysterious, and both also involve a special police force like team. Section 9 in Ghost in the Shell, and the STN-J in Witch Hunter Robin. While they share many differences, Ghost in the Shell and Witch Hunter Robin also share many similarities.
Witch Hunter Robin and GITS:SAC both follow teams of superhuman quasi-police specialized in hunting down special criminals (cyber-terrorists and witches, respectively). They combine stand alone episodes with an overarching plot to create a cohesive whole.