Magic Versus Science: sort of. The Imperial Elites rely heavily on magic, with limited technological understanding. The pirates are heavy on the technology, and have no access to magic. Both sides are presented with advantages and limitations.
Orcus on His Throne: Emperor Kreedor takes this Up to Eleven. So far he hasn't left his throne once in the entire comic. Not even gaining godlike powers has enticed him to actually carry out his evil plans himself.
Schedule Slip: In the beginning. Now is faithfully updated twice a week.
Took a Level in Badass: Everyone, very subtlety through-out the run. Originally, the pirates were only able to defeat the Sues by attacking them in their sleep and still needed to fight dirty and outnumber them. During the rematch at Kreedor's castle, they were only slightly outmatched while going one-on-one.
Unsound Effect: sound effects for gestures are common. Such as "nod" and "stand".
What Did I Do Last Night??: The series starts OFF with Tiren wondering that. Walter found her as a stowaway while she was sleeping. It happens a few more times in the story. (Hey, they're pirates. They get drunk)
Head Desk: Mary and Sue use their Twin Telepathy to debrief each other. When Mary goes off on a tangent about Elly, Sue does this to shut it off. It gets worse when Sue "calls" Mary and realizes she's talking to someone about when they went through puberty.
This Is No Time For Drinking: After getting the tech needed to find Tiren, Walter goes on a drinking binge, much to Leeroy's chagrin. Several strips later, Walter reveals that the engine runs on drunkenness. So Walter needed to be sufficiently plastered to work with it.
Noodle Incident: Leeroy did something with oranges and noodles. Lampshaded by Sal when she uses it as blackmail.
Drunk Driver: Subverted. Due to Walter's quirkiness and Applied Phlebotinum, the Cool Ship can only be driven while drunk. And he flys it perfectly well, until Marty makes Walter fly with his hands tied behind his back.
Word of Gay: Namely that Marty is straight. He's just absolutely sure that Elly is a girl.
Izor's Amazing Plan (Of Amazement)!
Batman Gambit: Izor pulls this with Sal in order to overthrow Kreedor. It involved Sal being sacrificed only to be "reborn" as the spirit of a god to grant Kreedor godhood. Izor would later assassinate him while his guard was down.
Properly Paranoid: Kreedor knows that Tiren is the best fighter. So, she is locked in a metal box, with all her weapons removed, and that box is suspended in air.
Raccoon In The Works: Not only does Izor's plan go horribly wrong by the timely intervention of the raccoon, but by himself when he alters an overly complex ritual. Izor knows nothing about magic theory. Unaltered the ritual would have killed Sal and nothing more. By altering it, the pirates' intervention, and the raccoon becoming an accidental substitute for Sal, the ritual flung everyone into another dimension and caused... well... we still don't know.