Title Screen Balls
On the title screen of the game, you can pick up the tiny black balls that are circling the World of Goo Corporation and play with them. The planet has gravity so you can throw them around to your heart's content.
Physics of Goo
In the level "Beauty and the Electric Tentacle", you can find a secret area with an image showing the "simplicity" of the physics of Goo.
Simply navigate the beauty ball to the left instead of the right, as shown in the following video:
Super Meat Boy
On the iPad version, one can look very hard to find Super Meat Boy hiding... in Super Fuse Challenge Time (who started the fire?).
Albino Pokey's New Easter Egg