Aborted Arc: The series ended one season short of its intended run, leaving several plot threads (including an arc involving the Cloaked Figure from episode 79) dangling.
Big Bad: In Seasons 1 and 2, It was Joel's future self. In Seasons 3 and 4, it was Evil. In Seasons 5 and 6 it was KOKOR And Stomach King. In Season 7 and 8, The Antagonist would have been Cassidy.
Breast Attack: "I'm going to specifically punch you in the nipple!"
Christmas Cake: Arguably Jessica, since she's technically middle-aged. Though whether or not she counts (she looks and acts like she's 25) is debatable.
Christmas Episode: Two of them. They're somewhat less heartwarming than the usual fare for this trope.
Coincidental Broadcast: Lampshaded in episode 49 when the gang turns on the TV, only to have a news reporter say, "If you've just joined us..." and then compliment the viewer on their excellent timing.
Downer Ending: Made even worse by episode summaries for the canceled final season having already been written and the whole thing planned out, then suddenly snatched away and replaced with everyone dying and the show itself being erased from time.
Which is then completely undone in episode 89, with Phil even questioning how he's still alive.
Episode 79 what with Rya's death and all.
Dropped a Bridge on Him: Mr. Malice is deliberately forgotten on Hydrox and blown up along with the rest of the planet. Not that anyone really missed him, though...
The same could be said for the virtual environment created by Joel at the end of the old Episode 87... yeah, thanks a lot, Phil!
Evil arguably qualifies as well, though he/she is somewhat less harmless than the Stomach King.
The Tandy Brothers, especially in their first couple of appearances. Even when they took over the world, they never really grew out of being harmless.
I Have Many Names: Shipmaster Greg Kevin Douglas Felix German Winslow.
Informed Deformity: Phil is treated as horrifically ugly, especially by women, despite not looking appreciably different from any other character. As with many character traits in the show, this is increasingly forgotten later on.
Its Pronounced Tropay: The fifth and sixth seasons were set on the "eShip": the "Spac" is silent.
Love Dodecahedron: Phil loves Elly (and Word Of God appeared to imply that had the series continued, the two of them would've become an item). Elly is stalking Joel and dating Andrew. Joel is dating Jessica, and is technically supposed to be June's boyfriend as well, though he doesn't seem to acknowledge her existence much. Rya and Cassidy are both pretty strongly implied to be in love with Phil; Rya was actually built to be Phil's girlfriend. Word Of God actually states that Cassidy was so obsessed with Phil that she killed Rya, viewing her as a threat to their love. None of this plays that major a role in the series, though (save for a few episodes).
Meaningful Name: The main villain in season 4's name is Evil.
MST3K Mantra: Invoked brilliantly in Episode 81 when Phil asks a whole bunch of questions about the nature of the virtual world. In this instance, the mantra is a bowling ball and it's application is it being thrown at Phil's face.
Nice Hat: Cassidy wears a pink striped top hat, which she has apparently worn since grade school.
No Fourth Wall: There have been episodes about why there isn't a plot-related episode today.
Not So Harmless Villain: Arguably KOKOR. Yet another Harmless Villain in the early seasons, he was unceremoniously killed off in season five. Season six had him rebuilt, with an entire armada of aliens backing him up. He even managed to defeat the heroes for several episodes, before Joel blew up the whole planet.
Planet Eris: Charismaville. Or rather, everything within Joel's simulated universe. Justified since, well, it's a simulation, so it's all intentional. Except when it isn't.
Robo Speak: Rya was voiced by a voice synthesizer for the majority of the series. Subverted with June, though there is some debate as to whether or not she's actually a robot.
Sanity Slippage: Jessica goes from one of the most capable characters in season five to a mentally unhinged lunatic in season six.
Screw Yourself: Joel once made Phil a girlfriend who was his female clone. Phil is greatly disturbed once he finds out.
Stalker with a Crush: Elly, with Joel being the object of her desires. Word Of God has stated that Cassidy is even worse, though she has a thing for Phil rather than Joel.
Phil arguably counts as well. He writes Fan Fiction pairing him up with her, for God's sake!
Hell, half the characters count. It's kind of implied that Andrew was stalking Elly as well.
Little Kuriboh has actually stated himself that he didn't start the abridged series idea, he just gave it a name.
Uncancelled: Came very close. After Matt Wilson announced that he was ending Bonus Stage a season early due to financial troubles, a fan offered to pay him $15,000 to continue the series. Nothing ever came of it.
Wacky Fratboy Hijinks: Episode 40, in which a fraternity (played by the cast of Waterman) moves into the house next door.
The plots to seasons 7 and 8 were changed around after season 6 ended. Perhaps anticipating that the series might not make it to an 8th season, Matt wrapped up several of the characters story arcs in season 7. He then left an option open for a more bare-boned (and therefore cheaper to make) season 8, with the 100th and final episode "Thank You for Playing" (in which every villain Joel and Phil had to face over the course of the series return to fight them, forcing the two to recruit all of their allies to counter the villains) being replaced by the much less ambitious "Trial Expires After 30 Minutes" (in which Joel and Phil confront the cloaked villain who killed Rya).
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