Bad Bad Acting: Luke and Cory's attempts to roleplay for extra experience tend to fall into this, especially early on.
Badass Adorable: Makino, the bartender from Luffy's flashback with Shanks, when the bandit comes in and starts breaking stuff. The GM had earlier threatened to call up the old "bartender is really a very high-level retired badass fighter" should the players start another bar brawl. Even more fun since the whole scene is played out by Luke alone (acting for everyone involved), so he basically invoked the GM's threat on himself.
Badass Normal: Nami may not be as statted out as Luffy and Zoro, but she's still able to pull off stunts that make Luke go "Holy crap, that's badass."
Calling Your Attacks: Made as a joke when Cory says to Luke, "What have I told you about calling your attacks?"
Chekhov's Gunman: Rika introduced herself by calling during a session. She later joined to play Medaka.
The GM has implied that Coby will become important in the future, as Cory's decision to concsciously abandon him will "bite [the party] in the ass."
Crossover: With Friendship is Dragons, wherein Applejack's player is revealed to be another of Cory's cousins, and he, Luke and Nat try designing their own characters for the pony campaign. Starts here.
Epic Fail: Invoked intentionally. Luke has a d20 with nothing but 1 on it, and uses it whenever Luffy has to make some kind of social skills check.
Every Episode Ending: Every time they finish an adventure, the Straw Hats call out "NEW MAP!"
Failed a Spot Check: Cory is so paranoid about this he constantly checks for traps.
Flaw Exploitation: The GM is a master of this when it comes to the characters' in-game Flaws. He's also able to pull this on the players themselves at times.
Half-Human Hybrids: To justify Zoro's insane Strength, Cory created him as 1/16th Fishman, 1/16th Giant.
Helmets Are Hardly Heroic: During the Devil's Tower arc, the GM figures that since helmets don't add to your Armor Class, Medaka is only wearing one to hide something about her character. She promptly accuses him of metagaming.
After using third-party books to pimp out Zoro to the point he's not accepted into the game at first, Cory gets stuck with Coby. Then, when Coby's being threatened by Alvida's thugs:
GM: By the way, thanks for bringing along those third-party books. They've got a lot of... neat character builds. Heh heh heh...
Cory: Uh... no problem...?
When building Zoro, he took the Undying Loyalty flaw, figuring it wouldn't come up since Zoro answers to no one. ...No one, that is, until he agrees to be Luffy's first mate. Cue "Oh dear god, what have I done."
Hypocritical Humor: When Medaka accuses the GM of metagaming, he casually asks her about a random monster. She immediately rattles off all of its stats.
I Know You Know I Know: Luke and Natalie engage in some back and forth thievery over the same map, escalating it in this manner.
In and Out of Character: Used regularly in the series. The GM is used to this, to the point of being shocked when they manage to stay in-character.
Kick the Dog: Discussed when Helmeppo bullies the little girl Rika:
Cory: Okay! We get it! He's the bad guy! Sheesh, man!
GM: Pfft, with you guys I can't be too subtle. Now watch him kick around this puppy.
Killer GM: He's the one who taught Luke how to min-max in the first place, after all. And he just loves playing to Luffy and Zoro's many flaws.
Line-of-Sight Name: Played with: after arguing about the validity of his first character design, the GM told Cory he could play him if he first came up with a name and character background. Then Coby gets his first look at Roronoa Zoro...
The Munchkin: Cory (Zoro) and Luke (Luffy). In the former's case, it got his initial character attempt briefly banned from the game. Given that the GM designed parts of the game with this in mind, this makes Natalie's life rather difficult.
My Name Is Not Zero: Luke has trouble keeping Zoro's name straight when they're first looking for him.
Mythology Gag: A couple of the questionable edits from the 4Kids dub get turned into wacky ideas the GM came up with.
Name's the Same: The little girl who gives Zoro riceballs is named Rika. That also happens to be the name of Cory's cousin, who calls during the Orange Town arc.
No One Could Survive That: Natalie deliberately invokes this during the fight with Buggy so that they can have the 'grand final confrontation' the boys were itching for.
Noodle Incident: Whatever happened to the GM's 'Mythical Sea Creatures' supplement in the past, he's still bitter over it when they start their latest campaign.
Off the Rails: From the moment he hears there's pirates in this setting, Luke immediately starts trying to derail the campaign, with Cory's support.
Phantom Thief: Nami is one. Somehow though, Luffy outdoes her.
Plot Armor: The GM puts this on Coby against his player's will, because Cory wants to kill him off so he can get a different character.
Precision F-Strike: Natalie after finding out half the loot was left behind.
Rouge Angles of Satin: The GM's handwriting is bad enough that Cory misreads his Knowledge Check about Roronoa Zoro. Later, he has to resort to texting Natalie when she tries to make Knowledge Checks about what Cabaji's saying.