The animation of Ghost in the Shell was performed by three different supervisors, namely Mamoru Oshii, Kenji Kamiyama, and Kazuya Kise. Although they are all based on Shirow Masamune's comics, there is no direct plot connection between the three supervisors' works (for now), and they should all be treated as parallel universes.
1. Watching order of Mamoru Oshii's works:
"Ghost in the Shell": the first theatrical version, The Puppet Master Incident, the most famous Ghost in the Shell work.
"Ghost in the Shell 2 INNOCENCE": The second theatrical version, the sequel to the first one, the events after Motoko left the Nine Sections.
On the whole, Mamoru Oshii’s two Ghost in the Shell films have an obvious personal style, which is relatively heavy and depressing, and the characterization is also relatively solemn. The main topic discussed is existential philosophy.
2. Viewing order of Kenji Kamiyama's works:
"Ghost in the Shell STAND ALONE COMPLEX": the first TV animation, The Smiling Man Incident.
"Ghost in the Shell S.A.C. 2nd GIG": The second TV animation, the sequel to the first TV animation, and an independent Eleven incident.
"Ghost in the Shell STAND ALONE COMPLEX: Smiling Man": the first OVA, a compiled version of the main plot of the first season of TV.
"Ghost in the Shell S.A.C. 2nd GIG: The Individual Eleven": The second OVA, a compiled version of the main plot of the second season of TV.
"Ghost in the Shell Stand Alone Complex: Solid State Society": The third OVA, the sequel to the second TV animation, the puppet incident.
"Ghost in the Shell Stand Alone Complex: Solid State Society 3D": The third theatrical version and the 3D remake of the third OVA.
3. The order of Kise Kazuya's works:
"Ghost in the Shell ARISE": The fourth theatrical version seems to be about the establishment of the Nine Courses.
Extended information
Chronology of the Ghost in the Shell animated series:
1995. Ghost in the Shell. Ghost in the Shell. Mamoru Oshii. Theatrical version 1. The Puppet Master Incident
2002. Ghost in the Shell: Stand Alone Complex. Ghost in the Shell S.A.C. Kenji Kamiyama. TV version 1. The Smiling Man Incident
2004. Ghost in the Shell: S.A.C. 2nd GIG. Ghost in the Shell Team S.A.C. 2nd GIG. Kenji Kamiyama. TV version 2. Individual Eleven Incident
2004. Ghost in the Shell 2: Innocence. Ghost in the Shell 2 Innocence. Mamoru Oshii. Theatrical version 2. Hadley's Rampage Incident
2005. Ghost in the Shell: Stand Alone Complex - The Laughing Man. Ghost in the Shell S.A.C.: The Laughing Man. Kenji Kamiyama. OVA1. TV1 main line condensed mixed version
2005. S.A.C. 2nd GIG Individual Eleven. Ghost in the Shell S.A.C. 2nd GIG: Individual Eleven. Kenji Kamiyama. OVA2. TV2 main line condensed mixed version
2006. Stand Alone Complex : Solid State Society. Ghost in the Shell SSS. Kenji Kamiyama. OVA3. The Puppet Incident
2008. Ghost in the Shell 2.0. Ghost in the Shell 2.0. Mamoru Oshii. Theatrical version 1 remake. Main It’s a picture quality improvement
2013. Ghost in the shell ARISE border: 1~4. Ghost in the Shell ARISE. Kazuya Huangze. OVA. Prequel work, The Origin of the Nine Lessons
2015 . Ghost in the Shell: ARISE ALTERNATIVE ARCHITECTURE. Ghost in the Shell AAA. Kazuya Huangze. TV version 3. ARISE re-edited, with new plot added in the last two episodes to connect with the new theatrical version
2015. Ghost in the Shell : The New Movie. Ghost in the Shell: New Theatrical Version. Kazuya Huangze. Theatrical Version 3. New Theatrical Version Based on the ARISE Series