When Jim and Dr. Doppler arrive at the space-port they get directions from two characters using a ladder. These are caricatures of the two directors: John Musker (at the top of the ladder) and Ron Clements (holding the bottom of the ladder).
The human characters are hand-drawn. John Silver's mechanical arm and the robot B.E.N. are flat-rendered CGI. The ship was created using Disney's 'Deep Canvas' process. In some scenes, all 3 types of animation appear simultaneously.
The first Disney film in which the maquettes (small character reference sculptures) were not made entirely by hand, out of clay. Silver's cyborg parts were constructed out of plastic, using laser technology.
The trivia item below may give away important plot points.
At the end of the film, Dr. Doppler and Captain Amelia (two aliens) got together and had children. A few lines cut from the film revealed that Dr. Doppler (the male alien) gave birth to the children. Disney ordered the lines cut because they thought males giving birth, even male aliens, was too risqué for a children's movie.