Timmy says "I wish Hubie was here." That is a reference to Ducky's line, "I wish Littlefoot was here." Then later he says, "Come on Hubie! You have to get up!" Is a reference to Ducky's line, "Come Spike! We have to stay together!"
Hubie is Similar to Mumble, and Marina is similar to Gloria. Both movies have the main characters fall in love. Both movies are musicals, both movies have the main character get chased by a leopard seal, and killer whales. Penguins in both use pebbles to get a mate.