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 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.
By starting a power transmission through ionization, Stark Industries were able to create highly charged storm activity. Their intention was to use it to store and transmit power. Since they were developing it for the United States Armed Forces as part of a weapons contract, they were essentially weaponizing the sky itself.
Having successfully stolen the Dataspine (an archived version of J.A.R.V.I.S.) and modified it with Project P.R.O.T.E.A.N., Kearson DeWitt of A.I.M. was able to create Ultimo. Merging himself physically and mentally with this giant A.I. through use of P.R.O.T.E.A.N., DeWitt was able to access all of the information archived by J.A.R.V.I.S., including Project Greengrid.
At an A.I.M. base in Malaysia, DeWitt/Ultimo put the project into effect, creating a typhoon. When Iron Man and War Machine attacked the base with a reprogrammed Arc Armiger, A.I.M. put up a fight with their soldiers and technology. Rhodes located the Greengrid power nexus beneath the epicenter of the storm. By repositioning the Greengrid relays and destroying the central power structure, he was able to send the generator into meltdown, terminating the project.
During the final battle against Ultimo at the Stark Archives, S.H.I.E.L.D. attempted to destroy it by using reprogrammed technology from Project Greengrid, but Ultimo took control of it and attempted to use it against them.
Project Looking Glass was a project spearheaded by Aida to create a living body using knowledge from the Darkhold. The device draws quantum power from Hell and converts it to living organic tissue, thus effectively creating a biological being.
Project Mr. Blue is S.H.I.E.L.D.'s name for their research on Samuel Sterns' mind after being mutated by the blood of Bruce Banner.
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 Patriot was a project designed with the goal of creating an enhanced individual who would serve as the new Director of S.H.I.E.L.D..
The Ultra Project was a project spearheaded by Church of Gibborim leader Leslie Dean, which consisted in identifying suitable victims to be sacrificed during the Rite of Blood in order to revive Jonah.
The Centipede Project is a super-soldier program organized and funded by HYDRA.
The Bio-Tech Force Enhancement Project was an attempt by the United States Armed Forces to rekindle Project Rebirth and recreate the Super Soldier Serum in order to form super soldiers as a response to the September 11 attacks.
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.
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.