Done literally in Astro City — the Confessor (a BatmanExpy) has a thing with former costumed crook The Stray, who is cat-themed.
Iron Man/Batmanexpy Tek-Knight in The Boys had this relationship with a Catwoman expy known as The Talon, and his partnership with his sidekick Swingwing deteriorated as a result after a threesome between them turned into a Love Triangle.
Dynamo5 : Deconstruction. Captain Dynamo had an affair with one of his enemies, a supervillain named Chrysalis, and had a daughter with her, who he helped raise. While Chrysalis herself said that they were in love, that did not stop her and her daughter from taking advantage of his death to impersonate him to increase their power base. Ultimately, Chrysalis, an amoral and ruthless criminal who is willing to murder anyone in her way, only escapes justice because of her affair with Captain Dynamo.
Subverted with the Ireyon in the Danish Paperinik stories - she comes on to our masked hero because she thinks he is Fantomius, her old flame, whose style and equipment is the base of the one Donald uses for regular superheroing. Donald isn't that interested, and vaguely annoyed she thinks he is as old as his grandpa. (She, on the other hand, is Really 700 Years Old.)
Played straight instead with Lola Duck, another female thief who often uses her beauty to take advantage during her work. Paperinik is not immune to her charm. Indeed, he just stops her attempted theft, but never arrest her. Despite they share a strong attraction, their relationship ends because of their respective roles.
Played with by Colonel Neopard and Commander Alyonesse: as mercenaries they're competitors, but at the end of the day, they'll date without an issue (Neopard even named his ship after her real name). Also, it's not clear who's the Catwoman, as they're both mercenaries, and while Neopard found himself fighting on Paperinik's side in both of his appearance that was just by coincidence the first time (Neopard's targets had a base on Earth and were allied with Paperinik's enemies the Evronians) and outright trickery the second (he was losing and needed reinforcements, and tricked Paperinik into coming to his rescue hoping he'd bring some powerful war machine), and in he's been known to fight for people who'd rather fight a war rather than pay for something they bought (his client before the job that brought him to Earth didn't pay their bills to a merchant coalition-or the mercenaries they used to defend themselves, hence why Neopard ditched them-, and in his second appearance he's working for a minerary company that wants to keep the industrial planetoid Grullop because the builders went over budget), while Alyonesse, in spite of being the enemy when she appeared, was fighting for Grullop's builders to recover the planet after the buyers refused to pay.
When inept superheroine Empowered met Thugboy, the love of her life, she was tied to a chair and he was part of the gang holding the hostage she was attempting to rescue for ransom. He whispered a few words of encouragement into her ear... and pulled her out of the way when one of her idiot teammates brought the building down. Empowered then lets herself get captured by his gang several more times just to have an excuse to keep seeing him. He does a Heel–Face Turn a few chapters later.
Played with regarding the titular Fox from The Fox Hunt and Dream Demon. They used to date each other back when they were both innocent kids, but have only just met again recently, well into their adult lives, with The Fox being married with children by this point, the youngest being in his teens.
In Jem and the Holograms (IDW) Kimber is dating the Token Good Teammate of The Misfits, Stormer. Stormer isn't bad or anything, but her band is constantly butting heads with Kimber's band.
In Johnny Saturn, Johnny Saturn I is married to Persephone, the daughter of Saturn's arch-enemy, Dr. Synn. Persephone is morally ambiguous and as likely to use her powers to aid her father as her husband.
In ReBoot it's suggested that Mouse and Bob had this relationship before he arrived in Mainframe. He arrested her when she tried to hack into the Supercomputer and Mouse flirts with him constantly.
The virus Hexadecimal also has a "thing" for Bob. He is polite with her, even going so far as to be a Friendly Enemy, but he still has to stop her from causing chaos through Mainframe.
In Sherwood, Texas, outlaw biker Rob Hood is romantically involved with Maria, the daughter of the Sheriff of Nottingham County.
The Spirit has at least three - Silk Satin, Sand Saref, and P'Gell.
Greyshirt of Tomorrow Stories has Lapis Lazuli. He really does love her, but, well... if they ever got together in any meaningful way, she'd probably kill him the second it went sour. Even she thinks so.
Witchblade bearer and cop Sara Pezzini and The Darkness bearer and Mafioso Jackie Estacado are rivals in their professional and supernatural lives, but as of First Born they have a daughter, Hope, together.
Star Wars: Legacy: Cade Skywalker was raised by his single father, Kol Skywalker. His Missing Mom turns out to be Morrigan Corde, an Imperial spy who fell in love with a Jedi Knight. They couldn't make their marriage work long-term because of their respective occupations and she left Cade with Kol when the former was two.
Downplayed in Black Hammer. Golden Gail entered a romantic relationship with her arch-nemesis Sherlock Frankenstein, but only after Gail had retired from being a superhero and Sherlock had already gone straight.
