Evil: "The flesh of the innocent has gone for too long un-rended, blood unboiled, families unseperated, school field trips unchaperoned!"
Artistic License - Geography: In Episode 76, Phil complains that people are ignoring the deaths being caused by Hurricane Katrina in the city of New Orleans "isn't part of America". When Joel points out that it is, Phil attempts to cover himself by claiming "New Orleans is one of my favorite states!"
Bad Future: In Episode 24, the ending shows the year 2005 ravaged by nuclear war and controlled by Rya. In Episode 31, Joel calls Phil in 2006 on his Time-o-phone but their conversation is cut short by a nuclear explosion.
Brick Joke: In Episode 50, Evil disables Rya in the middle of saying "which is why I have to kill you". Joel restarts her in Epiosde 51 after some modifactions...one of which was a Half-Life mod. When reactivated, she finishes her sentence of and incinerates Jessica with an energy blast.
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.
Con Man: Brad, originally (at the age of five, no less), and then Slim later on.
Deadpan Snarker: Rya, though most of the other characters indulge in their fair share of snark as well.
Death Is Cheap: So much so that in later seasons, it's not uncommon for main characters to die repeatedly in the same episode.
In one episode, Joel is about to be crushed by a giant robot. His last words?
Joel: "Well, see you next episode."
Apparently, Joel created a device which instantly clones the characters upon their death. He uses this to his advantage in one episode, where he tries repeatedly to jump into the eShip's filing service to fish out something list inside it. After trying to see if his corpses crush his fall, he gives up, and uses the duplicate money in the duplicated wallets of his clones to buy a replacement.
Disproportionate Retribution: In their initial visit to Hydrox, Joel slurs the local population by saying "If this place were a train station, it'd be called the Faggot Express". Though one of the natives says that they all are, in fact, gay, they are not outraged by Joel's display of homophobia but for "[informing] us of an antiquated form of transportation we don't have access to" and are sentenced to death.
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.
Future Me Scares Me / I Hate Past Me: Done both ways in the alternate version of Episode 88 (which starts as a reboot of Episode 25); future Phil thinks his past self is an asshole, and past Phil thinks his future self is a retard.
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.
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).
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.
Joel: Well, I guess that about covers our unnecessary '80s references for this week.
Show Within a Show: Occurs a few times. Episode 77 has Joel and Phil optioned by G4 to create their own cartoon for the network. The show is unfortunately ruined by Phil's endless inane suggestions, including several tropes.
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.
The Unintelligible: Mr. Malice speaks in music(not lyrics, actual music) such as the Mega Man Classic boss intro theme, or the opening to Ludwig van Beethoven's 5th symphony. He is apparently captioned in-universe as well as for the audience, as Phil can't believe he once subtitled "teh funneh".
Vague Age: Phil doesn't even seem to know his own age, as shown in Episode 64:
Joel: "Well, this little five-year-old girl over here threw out the lucky nickel. Phil. You...girl."
Phil: "That has nothing to do with anything! And I'm not five, I'm twenty-something. Or...fourteen. Or...fifty. I don't really know."
Viewers Are Morons: In Episode 60, while Joel explains why they're not doing a Bonus Stage episode that week.
Joel: "Now, as you folks know, our show is created by the INTERNET! But what you may not know is that our show is also powered by COMPUTERS!
Joel: "Good idea. The show is also done IN FLASH."
Vocal Evolution: And how. Joel and Phil's voices in particular go through some changes (they even switch voices in Episode 19), Rya goes from having a Synthetic Voice Actor to just having a robotic voice, Elly's voice changes to become more feminine-sounding, and Craig speaks slightly less droningly in his final appearance in Episode 89.
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).
With Friends Like These...: Joel and Phil, both show little care for the other in most dangerous situations (except for the occasional rescuing), and even when they're working together, they're constantly hurling insults at each other.
World of Weirdness: 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.