In 8-Bit Theater, issue #342 and #343, Black Mage and Red Mage debate who would win in a fight between Batman and Dr. Doom. Black Mage wins by pointing out that Doom would have one of these gambits set up. (The strips predate this wiki, so it wasn't a shoutout, despite the very on-the-nose choice of opponent.)
In The Last Days of FOXHOUND, the spirit of Big Boss temporarily possessed the body of his clone "son", Liquid Snake when he felt Liquid incapable of fulfilling his plans to free the world from the grip of an Ancient Conspiracy. As long as Big Boss has Liquid's body, he can move his plans forward himself. If the experience serves as a wake up call that motivates Liquid to wise up, become more capable, and win his body back from Big Boss earlier than expected... well, that just means that Liquid is better equipped to carry on Big Boss' legacy than he was before, and Liquid goes on to do just that until the end of the comic.
Okay, technically it's the same plan as in the game, but the rehash of Psycho Mantis's scheme to activate Metal Gear contains almost every feasible Gambit based trope (including pileups and Spanners mixed with dramatic irony for the reader).
Homestuck has this in the form of the massive number of time loops that are in it. Doc Scratch has manipulated the events of the story so that there is only one way everything could go. If any event happens that doesn't contribute to the arrival and rampage of Lord English, then the timeline reaches a paradox at some point. Paradox Space fixes this by killing everybody in the session shortly after failure is achieved.
Employed by Nale when he lures the Order to Cliffport by kidnapping Roy's sister Julia, then has his new Linear Guild attack. The Guild eventually gets defeated, but while they were distracted, Nale swapped places with his good twin, Elan — leading the Order to think they had won, when in fact the outcome was exactly what Nale had been seeking (his brother shipped off to jail and him safely undercover in the Order). Though wiping out the Order would have been a nice boast to his ego except it would mean that he could only defeat them when that wasn't his primary goal.
Redcloak outlines a much higher stakes Xanatos Gambit in the prequel story The Order of the Stick: Start of Darkness: he intends to capture one of the five Gates that holds back the world's Sealed Evil in a Can so his god, the Dark One, can use it to blackmail the other gods into giving the goblins equal standing among the player races (human, elf, dwarf, etc.). If he should accidentally unleash this Eldritch Abomination and unravel all of Creation in the process, the gods can then remake the world — but this time around, the Dark One would have a say in how the goblins were treated. Then again, even without the plan, the gods still need the Dark One - because he's a being that rose to godhood of his own volition and wasn't one of the four original pantheons, he has a unique color of creation, meaning that he's absolutely necessary to seal the rifts even without Redcloak's intervention.
Also played for laughs here. Tarquin calculates the financial gains he ultimately gets from his opponents even though they manage to flee, and adds in the price of the spear that they just threw at him.
Tarquin: Their every move makes my victory more complete.
Inverted in Book 7, when Durkon points out that Redcloak's options all lead to the failure of his plan. If he sticks to the plan, either the Order defeats him and his plan fails, or his plan to capture ths Snarl succeeds and the gods destroy the world (which would destroy all goblins and likely the Dark One as well). His only other option is to give up the plan altogether. Unfortunately, Redcloak doesn't believe Durkon thanks to the Sunk Cost Fallacy, and decides his best bet is to kill Durkon to deprive the Order of a valuable asset.
Charles, head of Charlescomm (one of the sides in Erfworld) is quite fond of this as seen by the discussion of the principle in this strip. "I got paid to turn it into a no-lose situation."
Weirdly enough, the titular amorph pulls off a minor one of these while investigating a mysterious human-cannonball-related death at a circus in this strip. Schlock's plan: hired reinforcements, or sent Jud Shafter to an early death. His friend considers both a plus. It was sort-of the former, but more accurately it became Schlock's ace in the hole while Schlock himself became the distraction.
Also discussed about Xinchub, when wondering if an assassin could actually get to him: "That man could turn his own death into an advantage."
Kevyn: I've done it myself. It hurts, but it's not actually that difficult. Tagon: ... Stop helping.
At the climax of volume 15, the protagonists realize that their hidden opponents have pulled a deadly Xanatos Gambit. (They're trying to provoke a Civil War in Sol System. Their brain-hacked troops are about to blow up a city of billions, triggering the carefully prepared conflict. If Earth's Navy attacks to wipe out those troops, it will look like they attacked the city — triggering the conflict.) Flinders is forced to acknowledge "Check, and mate. It's brilliant", to which Sorlie responds, "Before I die, I want to do something besides admire how much smarter than me our enemy is." Fortunately, not only has Flinders identified the threat in time, but the heroes have a Secret Weapon that enables them to Take a Third Option.
Joel Calley from Concession has his plan deconstructed. Some aspects of the plan have failed but not all of them and he has back up plans.
Heather in Misfile and the race she set up between Logan and Ash. If Logan wins, then Ash gets humiliated by losing to an opponent who had never raced before. If Ash wins, she winds up looking like a bully who took down a newbie. It goes wrong when Logan, in his inexperience, tries to pass on a curve and crashes.
In a chapter of Pearl of Mer, one of the Big Bad's lackeys shows he hates the group he is working with. He agrees to help the mermaid in getting her inside to take them down. But he also mentions if she does get caught, he ultimately did his job and brought them a mermaid.
In Darths & Droids, R2's decides to give Lando Luke's laser sword to fight their way out of the sarlacc pit, even though he's totally unqualified, because Luke refuses to use it. This inspires Luke to pick it up to defend Lando. When asked if this was the plan all along, R2 replies that it was sub-branch gamma-IV all along...
Gaia seems to have several Xanatos gambits running. Eldor appears to be running a centuries-long gambit intended to trigger The End of the World as We Know It. His primary tool may be running a gambit of her own if the way she scattered her friends to the places where they'd most likely function as Spanners in the works was her idea and not his. Finally, Gaia's chosen San de Vertis appears to be running her own gambit with King Savos to take over the world after "beating the evil out of Lillith". By the midpoint of the chapter Monster a Gambit Pileup seems inevitable.
In El Goonish Shive, Not-Tengu seemed to have one going in regards to Nanase's Guardian Form. To whit, his plan was: Bait Nanase into attacking him first. Not-Tengu believed Guardian Forms can only be used in self defense. If she isn't defending herself, she can't use it and he's free to form his flock without any worries. If she manages to use her Guardian Form anyway, still not a problem. Not-Tengu doesn't know her other spells, any of which could potentially beat him, but Guardian Forms locks all of those out for at least a day due to burnout. And while she is in Guardian Form, she can only fight in hand to hand combat, something he has no problem with. What ultimately derails his plan was not being able to actually catch the much faster Nanase and her girlfriend while both where in Guardian Form, followed by burning through the area's ambient magic causing himself to fall out the sky.
In Bob and George, Wily's original plan for Zero was a Xanatos Gambit: he designed the Maverick Virus to jump from Zero if he were ever defeated, infecting whatever hero defeated him. (Wily assumed this would be a Light-bot; it turned out to be Sigma, but the results speak for themselves.) This was a canon-compliant theory at the time. Since then, a lot of confusing Word of God has come down, and it's no longer clear what Wily put the Maverick Virus in or if he even created it.