The writers gave us the line "Jar Jar, you're a genius," and actually made it credible. See the monumental moment here.
The point in Phantasmal Malevolence when Maul starts to talk, leading neatly to the reveal of his true allegiance. Up until then the story had, with a few variants, been basically Episode I. And then Maul suddenly turns everything on it's head, catching readers off guard.
Jim roleplaying the scene where Anakin force-strangles Padme. For once, he's perfectly in character, completely serious, with no silly talk about loot or XP. His roleplaying is so superb that Annie actually asks him to stop for a moment, just to tell him how much she loves him for it.
The Darkest Hour of Episode III comes when Obi-Wan is the only thing standing between the antagonists and victory, not because he's the only player still alive, but because the other players are willing to allow the galactic conquest to happen since they'll be in a position of power when it does.
R2-D2: For crying out loud, Ben. The rest of us are okay with ruling the Galaxy. What part of that don't you like? Obi-Wan: I wrote "Good" on my character sheet and I jolly well meant it! Unlike some people!
The planet that Vader destroys not being Alderaan, but NABOO. They manage to write the sequence of strips before it, revealing the identity of Vader early (actually surprising people), making Tarkin a good guy opposed to this (again surprising the crap out of everyone reading the strips) and actually making this sequence go from "We knew this was coming" to a very heartwrenching, "He... he didn't?" moment because for the Darths and Droids readers, Naboo is has been a place they've become emotionally attached to. Oh. And JAR JAR WAS ON THE PLANET. Pete says it best.
The GM gets one in episode 778, when his and the players' characters are playing a game within a game: he predicted that Pete's/R2-D2's character would backstab his/Chewbacca's character at the first chance and loot his corpse, so he made sure it would backfire on him by putting a cursed item in his own coin purse.
Chewbacca: Let's discuss how you're going to pay for my resurrection, shall we?
The GM gets another one in episode 796 when Pete declares that he's going to hit the back doors he'd installed on the Peace Moon despite not being around there at all. He triggers an alarm doing so and the next episode has him constantly triggering one alarm after another.
To put this in perspective, Jim, the Cloudcuckoolander of the group, managed to brace a trash compactor with the very trash it was designed to compress, even though Annie had already pointed out how impractical that would be.
The revelation that Jim has been Obfuscating Stupidity the entire time since he was staying in character and wanted to convincingly roleplay his character as a guy who always comes up with idiotic schemes.
Lando decieves Vader and Boba Fett into thinking that Han has been killed by the carbon freezing procedure, saving Leia and giving him an opportunity to rescue her, Chewie and C-3PO and escape.
The writers wished to make The Reveal as powerful as it had been back in the theaters — they wanted the readers to feel what those having watched the film had felt, back in 1980, upon witnessing one of the greatest twists in movie history. They succeeded.
A two-parter: Not only has Pete apparently been writing an internally-consistent language for the beep sound-effect program for his phone since Episode I, Ben has actually been paying attention to this and taking detailed notes. This comes in handy near the end of Episode V when Ben is able to tell that R2's beeps don't match what Pete is saying and he realizes that Nute Gunray is still possessing him.
And then he tricks Gunray into plugging into the Falcon, which recently had a very powerful anti-virus program installed, freeing Artoo.
Cory (Luke) gets a big one in 1261. When the party is captured and about to be dumped into the Sarlacc Pit, Artoo (Pete) launches a Lightsaber towards Lando (an allied NPC) for him to use. After being maimed by a Laser Sword in cloud city, Cory (Luke) has developed a deep fear of such weapons, and correctly surmises that Lando will kill himself while attempting to use it. He immediately overcomes his paranoia, engages in a series of acrobatic stunts that nearly dump him into the pit, grabs the sword himself, and proceeds to kick ass with a weapon he is deeply afraid of.
Ditto General Grevious, though not to the same extent. The comic generally seems to have a habit of taking the more interesting characters from the movies and making them even more so.
1383: While captured by the Ewoks—who in this incarnation are greedy disciples of Nute Gunray—Sally manages not only to trick them into believing that C-3PO is Gunray & into releasing the party, but also to convince them to fight the approaching Imperials to defend capitalism.