Near the end of the movie when the the spaceship is landing, look in the wide shot of the crowd. In the middle towards the center left is one of the pigs from "Pigs in Space" sketch from the Television series.
After watching Muppets From Space again, I counted no less than 15 eggs -- and there are probably more that I missed. In order:
1) When the space-fish send Gonzo back to Earth, they shout out "May the Fish Be With You!", an obvious nod to "Star Wars."