Okay. The movie I'm thinking of had like.. two penguins, I believe, and one had an orange-yellow fluff of hair on the top of his head. They were trying not to get like.. eaten by sea lions, I think. I don't really remember what else was in the movie, but yeah. Lol. It was from either the late 80s or early 90s. Anyone have an idea as to what movie this is?

Possibly...

The Pebble and the Penguin (1995) (http://www.imdb.com/title/tt0114108/)

Scamper the penguin :)

Yes! It's Scamper. I have been searching for the same movie. And oddly, that is about all I could remember about the film too. Thank you.

I had that very same problem, all I could remember was that it involved two penguins, and a boat. And they were trying not to get eaten. Thanks guys! :D