If you use Kyrandia's transporters often enough, when Malcolm emerges at the Bluffs, he'll have a fly's head instead of his own. This is a reference to The Fly, a movie about a scientist whose genes get combined with a fly's in his machine, and he ends up turning into one.
Sometimes Faun will appear in the jungle swinging on a rope. This is what he did sometimes in Zanthia's hut in the second game, Hand of Fate, if Zanthia walked back into the hut after leaving the first time.
The points system was implemented in order to mock Sierra adventure games. There is no way to acquire all the points in the game.