In the Egypt stage, Mike finds the pizza delivery guy making his delivery while riding a turtle. The turtle is actually a Koopa Troopa, a common enemy found in Nintendo's Super Mario Bros. games.
The final stage of the game that takes place in the cave on C-Island is a recreation of the first stage of the original Startropics (1990), up until after the snake boss, where it branches off into a new section.
Leonardo da Vinci gives the protagonist a katana. This is a reference to the Teenage Mutant Ninja Turtles franchise, where the character named Leonardo uses Japanese swords.