Ephemural orchestrates one of these in TwoKinds. He/she/it erased Trace Legacy's memories in order to prevent him from killing a young Keidran girl named Flora, and then incited a number of incidents where Trace's Superpowered Evil Side emerged, generating mistrust between them, in order to eventually force Flora to return to her people and complete an arranged marriage with the prince of the Wolf Clan, thus uniting the Tiger and Wolf Clans into a force strong enough to resist the expansionistic human empire. The only thing that saved him/her/it from crossing over into Gambit Roulette territory, is the fact that he/she/it has displayed literally divine powers, and could thus conceivably have arranged every apparently coincidental incident. Unfortunately for him/her/it, somebody else had a stake in the plan as well...
In Looking for Group, it has been suggested that Cale's trials from his time in Kethenecia of the past to his return to the now-abandoned city with a group of followers is apparently a Gambit executed by the Archmage in order to create a new age for the city and prepare Cale to be a proper king. Technically speaking, it was supposed to be a solid plan, but a few things went wrong.
More recently, the three fiends played V's hunger for power, revenge, and personal glory quite magnificently against V.
A one page joke serves as an excellent example of the trope: This page shows Hayley dividing the loot. She has given herself nothing but five completely valueless rocks. The others suspect her of trying to cheat them out of valuable artifacts. They make her redivide the loot so she gets more gold, and loses out entirely on the rocks. The rocks actually are valueless -- she wanted more gold.
Xykon pulls one of these in the climax of Start of Darkness. Redcloak's brother Right-Eye is obsessed with destroying him, and has bought a magic knife that can deliver a sneak attack to an undead creature. Xykon knew about this, and protected himself accordingly. However, he still lets Right-Eye attack, knowing full well that Redcloak will kill his own brother rather than jeopardize The Plan. And now Xykon has proof that Redcloak will not betray him, will protect his phylactery, and will sink to any depths to see The Plan come to fruition; otherwise the sacrifice he made would be meaningless.
The commanding members of Starscream's Brigade do this a lot in the Insecticomics. Starscream pulled his biggest Batman when Thrust, unbeknownst to himself still under the virus-induced influence of Sideways, had the Constructicons build a Hydra Cannon to power up the Fallen. Starscream knew all about this and let it happen. However, at the last minute he swapped the Mini-Cons used to power the cannon with the knockoff Mexicons, which rather than amplifying the Fallen's power completely drained it. This left the servants of Unicron helpless to avoid having their afts kicked by the Brigade.
One of the main characters of Blur the Lines (also a very NSFW comic), Rick (who is a chubby chaser), is very good at luring overweight straight men into sexual encounters without making them realize he is doing so, such as when he convinced a straight man to give him oral sex to get back at his girlfriend, or when he bet a man at PAX that he couldn't roll four evens out of ten. (For losing that bet, Rick had to give oral sex to every fat man in the room.)
Lampshaded in Goblins. When Thaco challenges Dellyn to a duel, both of them know that Thaco has some sort of trap planned. Nonetheless, Dellyn accepts when Thaco points out that Dellyn's only two options are accept the duel, or refuse the duel, order his men to kill Thaco instead and live with the reputation of not being able to kill a single old, frail goblin, and Dellyn's ego won't let him pick the second option.
Doc Scratch on Homestuck is a Manipulative Bastard whose chosen MO involves "nudging" characters down paths they most likely would've taken anyways. For example, he exploits Vriska's spiteful nature and suggests that she kill Aradia in revenge for summoning the spirits of Vriska's victims to haunt her. He also deserves special mention for pulling a Batman Gambit on an entire species.
Terezi gives Batman himself a run for his money. Not only does she always know what everyone will do, but she also managed to manipulate Doc Scratch himself, not to mention Out Gambitting someone who can manipulate probability. It comes with the job: she's the Seer Of Mind, which means she can read people's minds and predict the future based on their actions.
In Darken, Baal targets the loved ones of Gort and Mink by taking possession of Gort's brother Tyr and murdering Mink's mother solely to make them angry. Then he "allows" a spy to be captured and has it leak false information implying that Baal's daughter is in Falloakes. Said girl is actually the daughter of Asmodeus, the most powerful Archdevil of them all. If Jill hadn't been there to reveal the truth to Gort and Mink, they would have unwittingly ruined whatever plans Asmodeus had for the surface and sparked a war between Gort's patron Mephistopheles and Asmodeus. Leaving Baal relatively squeaky clean and in a position to expand his own power base while his archrivals duked it out.
In Sluggy Freelance, Riff pulls one of these—on himself, sort of—to bring Zoe back.
Wonderella: "If anyone asks, I'm gonna say I did."
In Max Overacts this is how Janet convinces her mother to let her get her ears pierced. She convinces her brother to give his unrequited crush, Andi, a pair of fancy diamond earrings, knowing that Andi won't really want them and that Max will go to his sister for present advice. So Janet picks out the earrings for Jacob who gives them to Andi, who gives them to Max who gives them to Janet, who's mother agrees to ear piercing because it would be a shame to leave them in the box.
The Dip the Sheep storyline in Kevin & Kell. Rhoda is "expected" to eat Dip, the "sheepskin" she got her diploma on, but he's actually spying on Kell's company for Herd Thinners, so RL - who usually has real trouble seeing other animals' point of view, especially carnivores who show restraint - was counting on the fact that not only would Rhoda not eat him, but Kell would feel a responsibility to give him a job.