Project Greengrid was a project developed by Stark Industries. It was the company's first steps in developing the atmosphere's capacity for storing and transmitting power, essentially weaponizing the sky itself. It was later hijacked by Kearson DeWitt and Ultimo.
The Life-Model Decoy Program was a dismissed S.H.I.E.L.D. project set up to create a Life-Model Decoy, an android designed to act as a safeguard substitute for a S.H.I.E.L.D. agent. The project was eventually picked up and completed by Holden Radcliffe.
Operation Cerberus was a covert military operation aimed at eliminating terrorists stationed in Afghanistan and smuggling heroin into the United States.
Operation Paperclip, also known as Project Paperclip, was a joint Office of Strategic Services (OSS) / Strategic Scientific Reserve (SSR) program in which over 1,500 German scientists, technicians, and engineers from Nazi Germany and other foreign countries were brought to the United States of America for employment in the aftermath of World War II.
Phase 2 was a secret project created by S.H.I.E.L.D. to create weapons of mass destruction using the Tesseract based on HYDRA schematics.
Project G.O.L.I.A.T.H. was a S.H.I.E.L.D. scientific project led by Hank Pym and Bill Foster.
Project Master Man, also known as Mastermann Projekt, was HYDRA' s response to the Allied Project Rebirth during World War II. The project was led by HYDRA's top scientist, Dr. Arnim Zola.
Project P.R.O.T.E.A.N. (Picotech Regenerative Ordnance with a Tactically Evolving Adaptation Network) was a project developed by Stark Industries. The aim of the project was to create intelligent machines that could regenerate or modify whatever they were built for.
Project Reclamation was a secret S.H.I.E.L.D. operation designed to save the selected elite of the mankind in the event of a catastrophic event.
The Ultron Program was a global peacekeeping program, jumpstarted after the Battle of New York and designed by Tony Stark, to replace the Avengers. However, the program went horribly wrong, unleashing a genocidal machine hellbent on human extinction.
Project Deathlok was a HYDRA project conducted in cooperation with the Cybertek Corporation. It was one of HYDRA's several attempts to create Super Soldiers.
Project Destroyer of Worlds was a HYDRA project with which Daniel Whitehall intended to recreate a super soldier by designing an individual capable of taking on the properties of any known material.
The Winter Soldier Program was a top secret HYDRA project started by Arnim Zola that involved brainwashing American soldier James Buchanan Barnes and turning him into a deadly assassin for HYDRA using a serum similar to the Super Soldier Serum.
Project: Rebirth, also called Operation: Rebirth, Weapons Plus, the Bio-Tech Force Enhancement Program, the Erskine Program, and colloquially referred to as the Super Soldier Program was a highly-classified United States government project, the goal of which was the creation of Super-Soldiers to be deployed during World War II against the Axis powers.
The Avengers Initiative (a.k.a Phase 1; originally conceptualized as the Protector Initiative) was a secret project created by S.H.I.E.L.D. to create the Avengers, a response team comprised of the most able individuals humankind has to offer. The Initiative will defend Earth from imminent global threats that are beyond the war-fighting capability of conventional military forces.
Project Insight was a secret S.H.I.E.L.D. operation initiated in direct response to the growing need for national security that began after the Battle of New York. Agents required a Clearance Level over Level 8 to access the Helicarrier Bay in the Triskelion. It is presumed that only S.H.I.E.L.D. Level 9 and Level 10 agents know about Project Insight, as well as most likely most HYDRA agents undercover, posing as S.H.I.E.L.D. agents.
Project P.E.G.A.S.U.S. (also known as Pegasus) was the name of the joint project between S.H.I.E.L.D., NASA and the United States Air Force to study the Tesseract and harness its power. In the 1980s, project leader Wendy Lawson, who was in reality a Kree named Mar-Vell, used the Tesseract's energy to create the Light-Speed Engine in an attempt to end the Kree-Skrull War.
The Red Room, also known as the Black Widow Program, is a top-secret Soviet brainwashing and training program. The program takes young women and turns them into the world's deadliest and most elite assassins.
Project T.A.H.I.T.I. (Terrestrialized Alien Host Integrative Tissue I) was a S.H.I.E.L.D. Level 9 project ordered by Director Nick Fury and overseen by Agent Phil Coulson. It involved the harvesting of an alien corpse for medicinal purposes. The tangible results were only to be used if an Avenger had died.