The Martians sometimes land from the sky in patterns reminiscent of the Space Invaders.
The spider mech Dragon Nosuke in the third level of Metal Slug 2/X is an outright parody of the Metal Gear.
Metal Slug 3
In level 2 the boss drops a series of large black slabs with writing on them that some might say looks like the monolith from 2001: A Space Odyssey, which in Metal Slug 3D it's outright called "Monolith".
Mission 3 is one huge shout out to Metal Gear, starting out with a stealth mission and security cameras as the player proceeds into a secret robot factory.
There is an enemy on level 4 that looks like the brain eating bug from Starship Troopers.
In one of mission 4's secret paths there's enemies that look like Nausicaa's Ohmu. They are not as benevolent as in the movie.
The meat eating plants look like the evil plants from The Little Shop of Horrors.
The final level features small alien grunts who bear a striking resemblence to the tripod aliens from the musical version of War of the Worlds, which are themselves based on the description from the novel. (Yes, it did have a description for them. The only-showing-the-Tripods bit came from later adaptations)
This appears to be an ongoing theme with Japanese-designed Martians. Google around.
The final boss looks similar to E.T., though appearance is about where the likeness stops.
Also in the final level, the Martians have elite guards who look like Daleks of Doctor Who fame.
The submarine paths are most likely a reference to earlier game In the Hunt, right down to the part where you have to dodge lava. Another In The Hunt reference can be found in MS2, the China stage, where you have to avoid missiles coming up from the ground: in ITH the submarine had to endure a similar stunt. The visuals are pretty similar, too.
Also, the Slug Mariner looks suspiciously (and ironically) based on a little HELICOPTER (complete with vulcan cannon,but not placed the same way as the aforementioned Slug) from Battle Chopper, another game by Irem.