Okay, here's my brief rundown of the Ziltoid story.
ZTO: Ziltoid: "I am Ziltoid. Give me coffee or die, snot-eating hippie wart!"
By Your Command: Mostly told from what I believe to be the collective Ziltoidian army. The attack is imminent. The end is obviously by the human resistance.
Ziltoidia Attaxx: ATTTAAAAAAACK *SLIDE* DUGADUDU DUDU DUDU DUDUGADUDU DUDU DUDU
Solar Winds: Captain Spectacular reflects on his own existence and what he must do to stop Ziltoid.
Hyperdrive: I think this song is spoken by Captain Spectacular too because Devin uses a similar voice. It seems to be a love song, but it's also summarizing the trip during the hyperdrive before they land on Nebulo 9.
N9: The benevolent hivemind which rules over N9 (I think, I dunno) plants an idea in Ziltoid's head that he's basically worthless, crushing his ego.
Planet Smasher: Ziltoid's pissed and decides to proclaim his omniscience by destroying a planet. He is rejected by the Planet Smasher and his ego is depressed further.
Omnidimensional Creator: Ziltoid goes to the head of all existence asking what the meaning of his life is. "You gotta chill, man."
Color Your World: The omnidimensional creator warns Ziltoid that it's better for him not to know. After Ziltoid persuades, the creator tells Ziltoid that he is merely a puppet (in more ways than one, but for the purpose of the story he is a metaphorical puppet).
The Greys: Ziltoid's depression hits an all-time low. He is in fact a nerd.
Tall Latte: The story reaches its close and finds that the entire sequence was a dream by a lowly coffeehouse employee.
I've always thought of the story as a sort of allegory for a narcissist working in a corporate environment. I've also tried to justify it as an allegory for Devin's life as a musician, but that one falls apart pretty badly with the coffeehouse thing.