Simmons calls their mission a "Journey into Mystery," which was the title of the comic that debuted The Mighty Thor. The character was so popular, the book was eventually renamed for him.
There is a reference to Project Pegasus. In the Marvel Comics Universe, Project Pegasus (Potential Energy Group/Alternate Sources/United States) is a secret U.S. research project into alternative energy sources and a containment program for various arrested supervillains. It was referenced in The Avengers (2012) via signage in the bunker housing the Tesseract. Captain Marvel's powers are a byproduct of the project.
The aircraft and team are referred to as "SHIELD 6-1-6." In Marvel Comics continuity, the baseline universe is referred to as Earth-616.
In the 1960s, in the early days of Marvel Comics, "Lola"-style flying cars were often seen in S.H.I.E.L.D.-related issues. This is why Coulson said, "People tend to confuse the words 'new' and 'improved.'"
During the 15-day shooting schedule for the pilot, a splinter unit traveled to Paris, France to film part of Agent Ward's introduction. They had one day to prepare, one day to film, and one day to return.