Metal Slug 3 features a number of references to sci-fi movies. For example, Mission 2 features a guest appearance by the Men in Black. The carnivorous alien plants in Mission 4 are a parody of the sci-fi musical comedy, The Little Shop of Horrors In Mission 5, the squid-like aliens are a homage to the movie, Independence Day. Also in Mission 5, the alien clones you face seem to parody the sci-fi movie classic, Invasion of the Body Snatchers. Finally, the last boss battle seems to be slightly inspired by the ending sequence in Alien: Resurrection. One of the hostages (who also appeared in Metal Slug 2 & Metal Slug X) known as Hyakkutaro will join the fight by shooting fireballs.
Metal Slug 3 was the last game in the Metal Slug series that was developed by SNK. The stages that are set underwater are a reference to Irem's 1993 classic, In the Hunt. This is understandable as many of SNK's Metal Slug developers originally worked for Irem.