Actor Allusion: Scroop who was voice acted by Michael Wincott, who also played Rochefort in Disney's The Three Musketeers (1993) had the same line (word) delivered exactly the same way after the same question; "Transparently."
Onus (the six-eyed lookout), as the pirates find the treasure, does a Jaws reference: "We are going to need a bigger boat!"
The genders and looks of Amelia and Doppler's kids—3 girls resembling the mother, 1 boy resembling the father— was possibly a nod to Lady and the Tramp. That, or just brazen unoriginality.
After Silver's artificial leg is damaged in the course of the film, the ever-versatile cyborg extends a crutch from his also artificial arm and starts hobbling around just like Robert Newton from Disney's own 1950's version of Treasure Island. This also gives him a Primal Stance, making him more inhuman-looking.
The alien eggs Silver prepares in his opening scene are scaled-down versions of the alien eggs.