A number of episodes from the first season establish the origins of several long-running Marvel characters. Franklin Hall introduced in "The Asset" who becomes the super-villain, Graviton, and Donnie Gill in "Seeds" who becomes Blizzard, one of the foes of Iron Man.
The info given about San Juan, Puerto Rico is accurate. Even the legend regarding the "Garita del Diablo" is correct. Still today, no one dares to get inside of it although it's closed to the public anyway. Also the place marks exactly one of the corners of the Bermuda Triangle.
The character of Scorch is actually a mutant in the Marvel comics but since Fox Studios owns the rights to use the term mutants in Marvel properties, his status is alluded to slyly by using the slang terms used for mutants in the comics like "gifted" and "special".
S.H.I.E.L.D. stands for Strategic Homeland Intervention, Enforcement and Logistics Division. When originally created for the comic book in 1965, it stood for Supreme Headquarters, International Espionage, Law-Enforcement Division.
In an August 2013 Entertainment Weekly interview, Joss Whedon said that "Agents of S.H.I.E.L.D." is "basically a TV series of 'The Zeppo' [an episode of Buffy the Vampire Slayer (1997)], which was a very deliberate deconstruction of a Buffy episode in order to star the person who mattered the least. The people who are ignored are the people I've been writing as my heroes from day one."
The call-sign number for Agent Coulson's personal plane "The Bus" is 616, which in Marvel comic continuity is a reoccurring motif that is used to designate the universe which mainstream Marvel comic continuity takes place.
While this is a continuation of Coulson's first appearance (film or otherwise), this is actually the second television series that Clark Gregg plays the character. He also voices the character on Ultimate Spider-Man (2012).
There is a sign post in "The Hub" base that points to the H.A.M.M.E.R. hangar, a nod to the Spider-Man antagonist, Norman Osborn who for a time was in charge of S.H.I.E.L.D. and re-branded the agency as H.A.M.M.E.R.
"The Bus" is based on the U.S. Air Force C-17 Globemaster III transport plane. The real C-17 does not have the rear wings and engines of The Bus, though. If The Bus was real, it would have some severe design flaws. The rear engines would suck in exhaust gases from the front engines, and the rear wings would not generate much lift due to being in the wake of the front wings.
In Son of Origins, a book showcasing origin stories of various Marvel comic book features, Stan Lee admitted that the original Nick Fury, Agent of SHIELD comic book feature was inspired by the then-popular TV spy series The Man From UNCLE. HYDRA was inspired by THRUSH (itself inspired by SPECTRE, of the James Bond films) and in the second story, SHIELD was given a New York headquarters, with a secret entrance. In the UNCLE series, agents entered UNCLE HQ through Delfloria's Tailor Shop. In the SHIELD comics, the entrance to SHIELD HQ was through a barbershop, where the barber chair was lowered through the floor. The SHIELD comics and appearances would lead to use of the agency in the Marvel movies and the launch of the tv spy series, bringing the concept full circle.
During "The Well" Agent Simmons says that she is going to give Agent Ward 20cc's of Benzodiazepine to help calm him down. Benzodiazepine is a classification of medications, like Valium and Xanax, and not a medication itself. The use of this term is because Valium and Xanax are copyright-protected names.
The director of S.H.I.E.L.D. as of Season 4 is Jeffrey Mace played by Jason O'Mara. Jeffrey Mace was the 3rd Captain America in the Comics, and Chris Evans plays Steve Rogers' Captain America in the same Marvel Universe as this TV show. Jason O'Mara and Chris Evans have been on screen together in 2002's TV Movie "Eastwick"
The Bus's official call sign is the CXD-23 Airborne Mobile Command Station. In the U.S. military's alphanumeric aircraft designation system, "CXD" would stand for Cargo, Experimental, Drone Director. A more accurate designation would be something like XEV-23, for Experimental, special Electronic mission, Vertical Take-Off/Landing.
In the episode "The Singularity", Mack is in a bar while James is deciding his villain name. At one point he ponders the name Firestar. That is the name of Foreshadow who, in the comics, served as an Avenger and a New Warrior.
Both Clark Gregg (Agent Coulson) and Blair Underwood (Andrew Garner / Lash) appeared in "The new adventures of old Christine" together. Clark Gregg as Richard Campbell (Christine's ex-husband) and Blair Underwood as Daniel Harris (Christine and Richard's son's teacher and for a while Christine's date / "boyfirend")
A recurring event throughout the series is a fight taking place where one combatant is knocked out or disabled. The victor instead of killing them usually runs away or otherwise leaves the opponent so the opponent can fight again. An example of this is when Daisy shoots Grant several times but does not confirm the kill by shooting him in the head as she leaves.
Clark Gregg reprises his role as Phil Coulson. Although Phil Coulson was killed off in "The Avengers", Nick Fury used Coulson's death to motivate The Avengers after Coulson had appeared to had been killed by Loki, he was later revived from the dead on Fury's orders using a TOP SECRET procedure.
The 2014 poster for Agent's of S.H.I.E.L.D. appears to contain an easter egg. There are only 6 original members (Coulson, Fitz, Simmons, May, Ward, and Skye), but there are 7 pictured on the poster. It appears that Ward may be pictured twice, from two different angles, with a crack in the pavement separating one of his instances from the group, possibly teasing his double-agent role and eventual separation from the group.
Season 1 introduces the terrorist organization Hydra. Season 2 introduces Inhumans to the MCU. Season 3 introduces the Secret Warriors with Daisy (Quake) as a leader. Season 4 will introduce LMD's (Life Model Decoys)
Many fans responded to Brett Dalton (Ward) badly after his character was revealed to be a double agent. However, there is a large fan base on social media called Ward's Warriors who openly support the character and a potential redemption arc for him. They often trend hashtags like #standwithward during episodes.
This is the second MARVEL appearance of Glenn Morshower playing a U.S. military general who gets killed by another character overpowering him. He previously played Colonel Hendry in X: First Class (2011).
In May 2013, Ghost Rider rights reverted back to Marvel from Sony Pictures and first introduced in Season 3 was JT Slade, who is an Inhuman version of the grandson of Carter Slade - who was a ghost rider. So JT Slade is the first ghost rider introduced in series.
Though Dichen Lachman and Chloe Bennet play mother and daughter on the show, Lachman is only 10 years older than her TV daughter. However, this is appropriate, given that Lachman's character can prevent herself from aging.
Inhumans introduced in Season 2, is one of the least known properties of Marvel Comics and have been around for 60 years (2015) without any live action adaptation. This is the first property of Marvel Comics to be introduced in Live Action TV first, before Film adaptation.