A black hole from 'Cluck of the Dark Side'.
Revenge of the Yolk
Black Holes first appear in Revenge of the Yolk, in the Chapter 1 cutscene. A single Black Hole appears behind the Hero as he tries to defend himself against The Yolk-Star™'s attack. He ends up falling into it and teleporting to the other side of the Milky Way, 100000 light years away. From there, he tries to return to the Solar System to stop the Yolk-Star™.
Black Holes reappear in Ultimate Omelette, where they are still used in cutscenes.
Hen Solo Portal
Hen Solo uses one to warn the Hero of the recently finished Egg Cannon. He and the Hero use it again. The Hero ends up in the Foreign Galaxy, in the Chicken Testing Site, while Hen Solo emerges few star systems away.
Foreign Galaxy's Supermassive Black Hole
The Hero arrives there at the beginning of The Planetary Egg City chapter. After destroying the Planetary Egg City, Hen Solo arrives. He convinces the Hero to use it, which has him end up in the Retro Galaxy.
Retro Galaxy Portal
Supernova Galaxy's Black Hole
The Supernova Galaxy has a Black Hole which was still forming at the time the Hero arrived there. He used it, and he ended up in the Foreign Galaxy again.
Foreign Galaxy's Space Burger Portal
Milky Way's Space Burger Portal
This Black Hole is one of many owned by the Space Burger Corporation, which they use to deliver food to their stores in the Milky Way. The Hero used it to end up there, but he had to defeat the Iron Chef first.
Cluck of the Dark Side
Black Holes return in Cluck of the Dark Side, but this time around, they aren't used in cutscenes. Instead, they're used in used in Black Hole Skipping waves (Wave 8 and 99). Enemies in those waves, including Chicks, Chickens, and UFO Chickens, are able to travel through one Black Hole and pop out of the other one. The only way to destroy a Black Hole is to get rid of all of the enemies in the wave, after which they will poof. Touching a Black Hole without any enemies using it won't kill you (it used to in the Beta versions).