- The alien birth scene, in its own sort of way.
K: Congratulations Reg, it's a... squid.
- Although it being retconned to hell and back in the sequels sort of ruined it, the final scene where the newspaper showed the Agent K was reunited with his lost love and Agent J's simple smile at it.
- YMMV, but in an odd way, the memory J thinks up for Edgar's wife after she's been neuralyzed is kind of heartwarming. K makes up that Edgar ran off, and she'll decide she's better off, then J adds that she threw Edgar out because he never appreciated her anyway and now she's going to make a fresh start. Considering what little we see, it seemed like an abusive relationship, and the altered memory that she took charge and ended may end up empowering her in the future.
- In the beginning, a truckload of frightened illegal immigrants are stopped by Border Patrol agents. When Agent K steps in, he treats them courteously, welcomes them to the US and lets them go.
- "Men in Black" (the song) encapsulates the organization from the movie, especially the last verse. Yes, they're a heavily armed shadowy conspiracy group that wipes minds like cooks wipe kitchen counters, but they're entirely on humanity's side. It's a hard job, but it's worth it.