Inner Demons has a couple of metaphorical examples. First off, Rarity outright refers to Trixie willingly agreeing to serve Queen!Twilight in her evil in exchange for power as selling her soul. Meanwhile, Sweetie Belle and Scootaloo pledging loyalty to Queen!Twilight after she ages them up and gives them their Cutie Marks fits the thematics a little better.
Lucius allying with Gravemoss is presented in this fashion, since it is patently obvious that Lucius has, at first, absolutely no idea how bad Gravemoss actually is and it is heavily implied that Gravemoss is going to turn on him the moment he gets bored. To confuse matters slightly, Lucius procures theDarkhold for him in exchange for allegiance, meaning that technically, both do deals with the devil.
In turn, wielding the Darkhold opens one up to possession/enslavement by its owner, Chthon, who has been... making his presence known, shall we say.
The backstory reveals that Grindelwald made a series of these in order to increase his powers to (according to Loki, who would know) "godlike" levels.
Diamond Tiara agreeing to free Discord in exchange for him curing her mother's insanity (though to be fair, she didn't know who she was dealing with until the very end). Surprisingly, Discord actually keeps up his end of the bargain, but it seems that since he swore on His Parents, he didn't have much choice in the matter — and in any case, he managed to completely corrupt Diamond and break her to his will in the process, so he still screwed her over.
Dark World!Diamond Tiara made one with Discord: to be driven insane and become his first Dragon in exchange for being able to be with her mother. A resurrected Scootaloo takes issue with her because of this: unlike Discord's other minions, she chose to be his minion, but got off easy. To her surprise Diamond agrees with her.
Since the first generation cyborgs escaped their clutches early on in Young Offender, the Black Ghost organization gets clever when it comes to the second generation. Instead of simply kidnapping people to turn into cyborgs, they find ways to get them into their debt first; that way, if they think of backing out, well... Shame If Something Happened.
Much later on, things seem to have been set right... until Moriarty kidnaps Beth Lestrade and tells her he's about to kill Holmes, Watson, and the Doctor. Beth frantically begs him not to and offers herself as a willing slave in return for their life and liberty — a deal Moriarty agrees to, almost certainly understanding how much it would hurt Holmes.
The Nuptialverse: Chrysalis was once a normal pegasus, until Discord offered her the power of the three pony races in exchange for destroying the Energy of Friendship (the fires that destroyed the Windigos) to allow him to enter Equestria. Notably, Chrysalis thought that he was going to turn her into an alicorn; instead, he decided it would be funnier to make her a changeling.
Horseshoes and Hand Grenades, has the Serpents imposing deals in order to resurrect the people they want to contract with. For example, Shun, having been killed by Ryusei, makes a contract with Vasuki but he must live till the Earth's destruction, thus never being able to be with the people he loves. Shotaro gains one with Damballa to never be hurt again, but has his body transformed into one of a Creepy Doll and his sanity shattered along with it.
Helping Hoof made one with Checker. He never earned his Cutie Mark and was being hounded by his Abusive Parent Iron Hoof for it. So he agreed to work for Checker in exchange for her helping him fake earning a Cutie Mark and a job. Checker keeps her end of the deal, but Helping Hoof was reduced to little more than her puppet to torture as she pleases. In the end he gets free by finally helping expose her and turning himself in to the guard.
Terminal Justice has Batman beg Mr. Black, who the League believes to be Death (they're right, he just doesn't know it yet), to spare his butler Alfred. Mr. Black uses his fragment of a philosopher's stone to give Alfred roughly fifteen more years of life. He then goes on to kill Joker, Two-face, Scarecrow, and Riddler, seemingly as payment.
Hivefled; the Grand Highblood and the Condesce have a hobby involving inflicting Cold-Blooded Torture on teenagers, including their own descendant, and threatening the victims' friends until they sign over their souls. The ghosts of the two thousand plus victims are bound to a pocket dimension known as the Trap, until the Grand Highblood dies and hands them over to his patron spirit, who is apparently like him only more so.
Diaries of a Madman: Discord forcing Celestia into one with him kickstarts the plot of the story, and he later forces several other characters into such deals to suit his own ends.
Mega Man Recut has Dr. Light accepting funding from Senator King, who is in with the Syndicate. He is not aware of this.
The Attack on Titan fic My Child centers around a demon named Xaphan trying to get Levi to sell his soul to him, using every method he can to persuade him. However, Levi wants none of it and basically tells Xaphan to fuck off every time. He does eventually end up making a deal with the demon to save his son from dying in childbirth, and the story ends with him being tortured in Hell for it.
Tsali vowed to serve and follow Maledict if he would help the fox get revenge on the Seedrians. The Devil promptly turned him into a Demon Lord and revived him in exchange for eternal servitude. Also, Venus ritually sacrificed several of her fellow Seedrians to Maledict for the power to protect her people from Tsali. He answered, although not in the way she expected.
Bad Future Crusaders: Despite everything that Twilight Sparkle's actions cost her, Sweetie Belle still cut a deal with her new government in order to secure her own position as leader of the Diamond Dogs — gems mined by the Dogs were used to fund the creation of Environment Equestria, who in turn assured that the valley where the Diamond Dogs live always gets the right weather to ensure they can sustain an actual society.
Lay Down Your Burdens has an interesting example when Naruto makes a deal with the Kyuubi. Naruto doesn't want to be a jinchuuriki anymore and Kyuubi doesn't want to be imprisoned in a human, so Kyuubi teaches Naruto enough about seals that he can safely remove his seal and they can go their separate ways.
Uryuu does this in Alabaster Orchestra much like in canon, though his plans are apparently up in the air with Ichigo remaining loyal to the Emperor and refusing to assist him.
In A Protector's Pride, Yhwach made a deal with the ruler of Hell many centuries ago. Yhwach would stop aging and all of his descendants would inherit Quincy powers. In exchange, anybody killed by a Quincy goes to Hell, no matter their deeds in life.
In Who Is This Lord Tirek You Speak Of?, King Sombra gained his dark powers by sacrificing his blood relatives to Grogar. In the present, he attempts to keep the Mane Six as Sex Slaves so that he can have a steady supply of children to sacrifice and dramatically boost his powers.
Later subverted when it is revealed that Grogar has no interest in souls whatsoever. He agreed to the deal because he wanted to empower Sombra so that the tyrant could plunge Equestria into darkness, and due to things that Sombra was unaware of, Grogar had a loophole in the contract so that he could always do away with Sombra later if he proved ineffective.
In Being Dead Ain't Easy, Yami Bakura says he'll help save Joey if he gets the Millennium Puzzle in return. Joey adamantly refuses, so Yami Bakura makes an offer to Seto Kaiba instead—Joey's life for KaibaCorp.
The Count's World: Dimentio strikes a very Little Mermaid-like one with a shady Shaman in "Springtime for Dimentio," transforming him into a Boo (so he could court Lady Bow) in exchange for his voice.
How the plot of One Foot – Another Multiverse SI starts. After being run over by a train main character Poe makes a deal with Marvel's Mephisto to save his life not knowing who he is.
In Zelda's Honor, this is the underlying reason why Naar and every man in his army is able to revive from the dead moments after they die. Naar made a deal with Barrachas, a Hunger demon of the old world, loyal to Demise. In return for immortality, Barrachas requested Naar to spread the war to Hyrule and other lands to continually find fresh bodies for him to further link together using shards of the Fierce Deity Mask. This accumulation of souls would eventually be used for the revival of Demise.
In an untitledEver After High fic, Milton Grimm offers Raven and Briar a deal: they can abandon their inherited destinies (which are both very bad, in different ways) if they take up each other's. They agree, but the resulting Bad Future is only slightly better than it would have been otherwise (and perpetuates the oppressive Legacy system).
In The Bridge, Bagan gathers several Kaiju and offers them several boons if they agree to serve him. When Grand King Ghidorah and Legion tried to tell him to shove it, his response is to send them all to their knees in pain and threaten to kill them where they stand if they don't accept. Once they accept, he keeps his word and grants them their boons. He's still screwing them over, because he told them that they would conquer the universe under his leadership, but he's really an Omnicidal Maniac and he's just biding his time until their efforts allow him to regain his full strength. Once that happens, he plans to wipe out all life, including them.
In Father Goose and the Black Knight, Xander and his Slayers sometimes offer demons and vampires a deal for information. The reward varies from getting a pass the next time they meet to, when they're truly desperate, picking up their tab for the next month at a given demon bar.
Will/Van first makes contact with A'lek'hol'an during a near-death experience. He offers to save her and give her enhanced magical powers, in exchange for her becoming his avatar. Not having much of a choice, she accepts.
Phobos later frees Tracker from his imprisonment and offers him a job hunting rebels. The undead hunter agrees, but does not actively submit to Phobos' control.
In The MLP Loops, Pinkie Pie offers one of these to Svengallop once he finally pisses her off enough. Applejack immediately leaps in to stop the deal, and states that while Pinkie Pie can deliver, it's a bad idea all around. Sure, he'd get his soul back next loop, and probably no more tarnished than it already was, but it's the principle of the thing. (Pinkie just wanted a spare soul as a chip for the next time she and the Warhammer 40,000 Elder Gods had a poker night.)
In the story A Dream, the main character Valiant brings himself back from the dead by making a deal with the most beloved entity he could find: Santa Claus. He briefly wishes he had made the deal with The Beatles instead.