Young Agent K is wearing the watch that will become the light source for the Grand Central Station locker creatures in Men in Black II (2002). This can be seen clearly when young Agent K and J are having pie before the Mets fans enter.
The zip line escape system shown at the Apollo launch pad really did exist. It was installed for the Apollo program and enhanced for the Space Shuttle program. In some pre-launch emergency scenarios, the crew would have ridden steel cages down the zip lines to explosion-proof bunkers. Astronauts practiced using the system as part of their training, but it was never used in an actual emergency.
This is Will Smith's first film in 3.5 years, since the release of Seven Pounds (2008) in December 2008. This is the longest he has gone without appearing in a movie since his film career started in 1993.
Although the World Trade Center Twin towers are already standing (but still under construction) in 1969, they cannot be found anywhere in the 1969 parts of the movie, but the Freedom Tower (or One World Trade Center) can be seen under construction in 2012 near the ending of the movie.
According to the trailer Agent J travels from 2012 to 1969, 43 years into the past. He wakes up and sees a young Agent K, played by Josh Brolin. Brolin is only 21 years and 5 months younger than Tommy Lee Jones, who plays the older Agent K.
BugEyes, the fictional "creator" of a fake blog (source: www.themeninblacksuitsarereal.com) about investigations concerning the Men in Black, made a cameo in the film as an MiB agent in the background.
When Jay exits The Chrysler Building in 1969, he is facing The Roosevelt Hotel. In 1969, the hotel across the street from The Chrysler Building was the Commodore Hotel. Opening in 1919, it was completely rebuilt, including being completely covered with a glass façade and reopened in 1980, as the Grand Hyatt Hotel. The Roosevelt Hotel is at the corner of Madison Avenue and 45th Street. Opening in 1924, it would have been a better fit for 1969 New York City than the modern glass covered Grand Hyatt.
At 47:20 into the film when J is in the large neuralyzer, the SFX you hear when the machine is shutting down is the same SFX from The 'burbs (1989) when the Klopek's are in their basement and Art, Mark and Ray are spying on them from outside (at around 27:50) - This claim has since been dismissed by the film's sound designer...
When Jay enters the music store, the clerk behind the counter is playing air guitar (and singing the wrong lyrics) to the Black Sabbath song "Children of the Grave" from their 1970 album "Master of Reality".
Yuri Lowenthal: the voice of Knuckles the graffiti alien in a deleted scene (which is shown in the trailer), had voiced Ben Tennyson in the Ben 10 (2005) cartoons; the Tennyson family is connected to the Plumbers, an organization similar to the Men in Black.