Expy: Zurg may be one of Bowser of all people; he's the series eponymous character's greatest enemy, he self-identifies as Evil, he tries to conquer everything he lays eyes on, he always shows up at inopportune moments to make things worse, he always comes back no matter how many times he's defeated, he's responsible - or at least related to - pretty much anything villainous that happens in the series, and he even has horns! If Bowser ever tried on a Darth Vader suit, the two would be virtually indistinguishable.
Zurg: And if I may remind you, no gianttrash compactor! When heroes fall in, they always have enough time to figure a way out! Make it an incinerator!
Gainax Ending: How does the final fight between the Galactic Alliance and the Evil Empire conclude? Does Warp Darkmatter return to Star Command? Do Mira and Romac live happily ever after? Is there a connection between Jessie from Toy Story 2 and Dr. Ozma Furbanna? The series never actually had a formal conclusion.
Genius Bonus: Natron the First, the "Living Mummy". The mineral natron was one of the important ingredients in the mummification process in Ancient Egypt.
Also, to get to Planet Roswell, you need to go through the Mogul system. A Project Mogul balloon was said to be the cause of the Real Life Roswell Incident.
Harsher in Hindsight: In "Eye of the Tempest," a mutated super villain wrecks a power station made up of two generating towers. The first one is damaged without much comment... But as the second comes down, Mira shouts, "Look out! The other tower!" amid falling rubble. Chilling in hindsight, as WTC North would do the same less than a year later.
Hilarious in Hindsight: The show does a episode (one of two actually) with Buzz and Booster crash landing on a world called Roswell where they're the aliens and the residents are the stereotypical green/gray alien the media usually depicts. (green skin, blacks eyes bald head, etc) Yet their town is effectively just like a normal human town. A few years after the show ends its run, a movie called Planet 51 is made detailing...you guessed it (though their aliens are different looking the premise is the same). What makes it funny? It's a CGI movie made by another company and this show was co-produced by Pixar, whose forte is CGI movies.
Wayne Knight voicing Zurg becomes especially hilarious when one remembers that the wrong Buzz Lightyear once speculated that Al, who was also voiced by Wayne Knight, was one of Zurg's minions when they inform him that he was the guy who kidnapped Woody in Toy Story 2.