DC once printed an Elseworld story (back when they were still called "Imaginary Stories") where Lois Lane had been killed after Superman settled down and had a daughter with her. At one point, he created a robot duplicate of her, which proved to be all too lifelike. Apparently, Uncanny Valley doesn't faze some people.
Toyed with in Frank Miller's The Dark Knight Strikes Again, where Hal Jordan whose control over his powers now renders him virtually omnipotent, has left Earth and is now living on Mars, where he lives a happy, wholesome family life with his wife and son. Unlike most examples of this trope, the Martians are not rendered physically attractive or appealing in any way; Hal Jordan instead uses his power to make himself a Martian, completely capable of maintaining the form indefinitely, as well as capable of breeding with other Martians, and is extremely reluctant to return to Earth after receiving Batman's transmission, until his wife urges him to help his own people. He only reverts back to his human form after he has already left Mars, and is quick to return as soon as his business on Earth has been finished which involved him multiplying his size to that of many times the Earth, able to grasp the entire planet in his fist, crushing Lex Luthor's planet wide multi-trillion dollar WMD satellite network while leaving the planet itself unharmed.
John Stewart married Katma Tui (alien) and had a long-standing relationship with Merayn Dethalis (also alien).
The Green Lantern Corps seems rife with this. Hal Jordan and Arisia, Kyle Rayner and Soranik Natu, and when you bear in mind that nearly every member of the Corps is a different species, when relationships between members of the Corps were banned over 200 resigned in protest.
Legion of Super-Heroes: there are a lot of interspecies romances in the Legion; some of the more notable are Brainiac 5(Coluan)/Supergirl (Kryptonian), Colossal Boy (Human)/Yera (Durlan).
Just about all major cast relationships are Cross-species; the Legion is compromised of tons of different species hanging out together 24/7, almost all raised with no species boundaries whatsoever.
Mossy earth elemental Swamp Thing and his human wife Abigail Arcane. Played with considering the nearby town finds out and convicts her of bestiality. Abby flees to Gotham City where the police hold her, causing Swamp Thing to go ballistic to free her. Batman finally talks the Mayor into giving in considering that if he wants to hold Abby for having a relationship outside their species, then he'd better arrest half the superhero community - such as the Martian, the Tamaranean, and, oh, that guy in Metropolis. The Mayor's expression conveyed all that needed to be said about how insane a move that would be.
Since Kryptonians are all but extinct, this is the only kind of romance Kara can have unless she is willing to commit incest. Among her first boyfriends were Dick Malverne (an human), Brainiac 5 (a green-skinned Coluan), and Jerro (an Atlantean merboy).
Post-Crisis universe: In addition to Brainiac 5 (mentioned above), she had a quasi-romantic friendship with Captain Boomerang (human) and a short-lived relationship with Apokolips native Power Boy. And had a crush on Dick Grayson, but that hardly counts.
Subverted in Elseworld's Finest: Supergirl & Batgirl. Most people think Supergirl and Lex Luthor are together, but their relationship isn't romantic at all (and non-existent after the events of this story).
In Many Happy Returns, human Supergirl Linda Danvers and Silver Age Superman fall in love and get married.
Nightwing and the human/alien Koriandr of Tamaran, aka Starfire, in at least one continuity of The DCU. She was the first of his girlfriends that he was quite blatantly implied to have had sex with, they've been engaged at least once, and they were even almost married once — as in, the only reason they aren't husband and wife is because fellow Titan Raven attacked the ceremony and killed the minister before he could complete it. Though they are drifted apart in modern continuity, both still remember and occasionally flirt with each other over their former connection.
Deadpool briefly was married to an alien woman named Orksa who resembled a anthropomorphic yellow hippopotamus. They divorced on good terms so she could be with someone who loved her more than he did. Both her previous husband and her next one also appeared to be different species than her. He later got married to a Succubus named Shiklah, who though she can appear mostly human, is actually a huge purple demon. Deadpool met her when Dracula hired Deadpool to bring her to him for their arranged marriage.
In Fantastic Four, Johnny Storm and his former wife Lyja. Johnny had thought that she was human when he married her - she's a Skrull. In the Marvel Comics 2 Universe they are still married and have a son, Torus.
Rocket Raccoon (take a wild guess what he is) and quite a wide variety of alien species. In his original mini-series, his girlfriend was Lylla (anthropomorphic otter). In his 2014 series he has been shown to have a brief relationship with Princess Lynx (alien, cat-girl). In the 2014 Guardians of the Galaxy annual, Rocket is shown to have 3 sons (which he insists are nephews) whose mother is clearly some sort of blue skinned alien.
The comic Howard the Duck had Howard (intelligent talking duck from an alternate reality) and Beverly (human). This was played way too straight in the movie.
The Incredible Hulk (gamma-irradiated human) with Jarella (from K'ai) and Caiera (Shadow Person). He had two sons from his relationship with Caiera.
Namor (human/Atlantean hybrid) married Green-Skinned Space Babe Marrina, but also found time to pursue the human (and all-too-married) Invisible Woman.
Namor and that lake-monster queen from Tabula Rasa
Hope: Ick! Ick! Ick!
Namor: You are only showing your parochialism and prejudice. She is a dignified queen of a noble people. Namor is nothing if not cosmopolitan in his tastes.
Also, there's been flirting and suggestions of future hookups between Namor and Hepzibah (an alien skunk woman. Well originally a skunk woman, a lot of artists these days tend to draw her as a Cat Girl or even just a palette-swapped human, but whatever).
Atlanteans in the MU are a branch of the human race, so this would me more like interSUBspecies romance.
Namor, as implied above, is the result of one of these pairings: human father and Atlantean mother. His cousin Namora has a human mother and Atlantean father. As they're effectively the only members of their kind, most any romance they pursue (aside from each other) is one of these.
Nova (human) and Green-Skinned Space Babe (literally) Gamora, in Annihilation. Before (and after) Gamora, Rider was with Namorita (Atlantian Mutant/Clone). Namorita's metamorphosis into Kymera (much less human looking form, resulting from her ancient Atlantean DNA) didn't ruin this relationship.
Depending on which origin story you actually believe, Rictor (human) and Shatterstar (alien-ish.) are this.
ROM: Space Knight was in love with the Terran Brandy. On the plus side, Rom is a Galadorian, basically a branch of the human race. On the minus side, he'd been cyborged into an all-covering suit of plandanium armor. On the plus side, it was theoretically possible for him to become a normal man again. Still, whether Rom and Brandy count as an interspecies liaison is a judgement call.
Karolina (Majesdanian) and Xavin (Skrull) in Runaways. When Xavin was Put on a Bus, Karolina and Julie Power (human) started going out.
The former might not be an example, since the Vision might have been designed to be compatible. Is an artificial person of human design a different species? As for Crystal and Pietro, the Inhumans and mutants are two branches of one breed anyway, so that doesn't really fit the trope.
Later, Crystal was remarried to Ronan the Accuser (Kree).
Werewolf by Night's Jack Russell (a werewolf) has had several long term relationships with human women.
Professor Charles Xavier and the Shi'ar Empress Lilandra. Made worse by the fact that Lilandra is descended from avian stock, Charles from primate stock. OTOH, the Celestials might have reengineered both breeds to make them compatible. The Shi'ar seem more primate-like than evolution would plausibly manage...
For a long time, Dazzler (human mutant) and her husband, Longshot (interdimensional alien). Since their divorce, Longshot seems to have jumped on the Boldly Coming bandwagon of interdimensional relations.
Nightcrawler (mutant) and Cerise (Shi'ar).
Astonishing X-Men: Beast/Brand. Complicated, since he's a human mutant who became more animalistic as he got older and now looks like a giant blue cat, and she looks mostly human and is actually half-alien. Apparently her dad was a huge blue furry thing, which takes it into even more perverted territory.
One of the most exteme cases in the Marvel Universe was Thena (one of the Eternals) and Kro (one of the Deviants), a true Monatgue and Capulet romance, seeing as their two races were sworn enemies.
2000 AD'sLobster Random ... a mechanophile. That is a (modified) human who is sexually attracted to robots. And not human looking robots either...
It expands to "No Biomechanical Barriers". The same arc suggests Bunnie, who is robotic from the waist down, will have children, too!
Actually in certain continuities, Belle and Jacques (Bunnie's kids) could actually be born normally (so to speak) as Bunnie is cured of her robotization...though given that plotline, some fans will likely ignore it.
It is averted in the case of the Iron King and Iron Queen, a massive ox-man and ordinary human woman respectively, whose "marriage" is purely an arrangement of political convenience; the writer acknowledged that having a human and animal character wed "might raise some eyebrows".
Astro City has Rex and Natalie of the First Family. He's a giant orange dinosaur monster with rocky scales and the prince of Monstro City; she's an energy being who internalizes her powers to become a Size Shifter giantess.
There's also Duncan Keller, aka the hero Starfighter, who's married to alien empress Illula. They have two children, a son and daughter.
There's a children's comic called Mr. Badger and Mrs. Fox, it's meant as An Aesop about blended families.
Pretty much the point of the Barbarella comic strip and carried over, to a lesser extent, in The Movie.
B.C. has John the tortoise and Dookie Bird, who also had a fling with a pelican at one point.
Buck dismisses Louisa, who is human, (albeit of a different sub-species), who has been modified to be irresistible to men as "too skinny". Of course, there's also the small issue that Hoffmanites like Buck, coming from a high-G world, tend to find other humans "too fragile". Meanwhile, the above-mentioned Ms. Louisa Dem Five proudly runs a multi-species brothel...
He also, when dropping in on his alien bartender's girlfriend sunbathing in the nude comments that "You aren't compatible with humans! I don't even know which bits I'm supposed to be looking at!" He then gives her some very specific compliments.
In Circles, there are few repeated species. One exception are Doug, his ex-fiancée and their son, who are all Otters.
Crusader Adam of Destine (later simply Adam Destine) and the djinn Elalyth, parents of the Destines in ClanDestine.
In the Donald Duck comic "The Old Castle's Secret," the jewel thief Diamond Dick claims that he knew about the hidden McDuck treasure because his "third wife was a McDuck on her great grandfather's side." Diamond Dick is a dog. Apparently something... interesting... has been going on in the McDuck family tree.
ElfQuest: I'm gonna have to spoiler this whole thing because it involves a major plot revelation. In ancient times Timmain (super-advanced humanoid alien in elf form) shapeshifts into a wolf and mates with the alpha male of a wild pack. result: Timmorn Yellow-Eyes, half-elf, half-wolf and father of the Wolfrider tribe. Many generations later the pure-blooded elf Winnowill views the Wolfriders' origins with disdain, asking the pertinent question: "Do they renew their kinship even now?"
This disdain is hypocritical since Winnowill is soon revealed to be the mother of Two-Edge, who is half elf/half troll.
There are also some attempted human/elf pairings, which generally go badly because the elves' "bloodfire" is too intense for humans, although centuries after the main storyline the shapeshifting elf Jink enjoys a number of successful partnerships with humans of both sexes. Since she does seem to have a weakness primarily for telepaths, it may be that the elf/human compatibility issue involves a psychic element...that, or she just has worked out the kinks through experience.
Bufkin and Lily Martagon are a unique example. He's a flying monkey and she's a tiny fairy-like Barleycorn Girl. She considered herself his girlfriend, but he didn't reciprocate any romantic feelings due to the species and size barriers. However, in the epilogue of their story, it's revealed that on several occasions throughout their many adventures in Oz, one or both of them were magically transformed into compatible species. During these times, they got married and had many children. At the end of their lives, they were still living together and in a very loving relationship despite being in their original forms.
The downsides to be explored a bit more in others. For instance, one story features a Gotal who enjoys sleeping with members of other species. Or he did, until he slept with a female from a species that eats the male alive after sex.
The Rogue Squadron series had a romance between a Calamari and a Quarren: Romeo & JulietIN SPACE!, in short. And in one arc it was implied that Janson and Hobbie slept with a pair of Bothans.
One of the most prominent romances of the Clone Wars comics was between Jedi Masters Tholme (human) and T'ra Saa (Neti). Neti are extremely long lived, shapeshiftingplants.
At least one of the comics set during the prequels had a fair bit of Ship Tease between the aquatic Kit Fisto and Twi'Lek hottie Ayla Secura. Talk about Naughty Tentacles...
It's pretty much taken for granted in the Star Wars universe that Twi'lek women are desired by males of all species - and yes, it often really is due to their "naughty" lekku, which can be trained to perform sensual functions. It was used rather disturbingly in A. C. Crispin's novel The Hutt Gambit, where a young Han Solo is (to his chagrin) leered at by an elderly female Twi'lek.
Cade Skywalker (Human) and Deliah Blue (Zeltron) from Legacy.
Lucien Dray (Human) and Q'Anila (Miraluka) from the same series.
Oh, Tank Girl, as if your sociopathic heroics weren't enough, you also have to get involved with Booga. The mutant kangaroo. And then cheat on him with your tank... Yeah, it's that sort of comic.
The Archie-published Teenage Mutant Ninja Turtles Adventures featured three such relationships. The first two involved mutant turtle Raphael, who became involved with two mutant fox women at different points of his life, and even ended up marrying one of them. On the other hand, there was the relationship between musician Mondo and his girlfriend Candy Fine, which persisted even after Mondo was turned into a mutant gecko.
Not to be left behind, the original incarnation of the TMNT has featured two different interspecies romances. The first occurred between Michelangelo and "Seri" (reptilian alien), while the second will occur between Leonardo and human superheroine Radical several years into the series' future.
Warlord of Mars has it all over the place, but most prominently is the main couple: John Carter (an human from Earth) and Dejah Thoris (Red Martian). Other examples include Thuvia (also a Red Martian) and Phaidor (White Martian) being attracted to Carter, while Salensus Oll (a Yellow Martian) takes all three aforementioned ladies as his concubines, though in his case its more like one-sided perverse lust than true romance.