From this gallery page, A New Life Era, and Moe and BIOS birthday party, there is heavy speculation about this between between Amy Jr. and Moe. The Recovery Part 2 shows there MIGHT be some romantic love between the two. However, they're both very young, and may not be each other's soul mates. For all we know, Bertha might be Moe's soul mate, although The Hacker probably wouldn't be too happy about that.
Lucia and the first William Adama in Fail Better. She's a goddess, he's a dead human, they meet in the underworld, get married, become the "parents" of generations as ancestor and step-ancestress respectively and "live" happily forever. After some complications.
Selene and Billy too. Apparently falling in love with humans runs in the family.
Next to Dale & Foxglove and Chip & Gadget, The Midnightverse hints at something growing between Sparky (rat) and Lahwhinie/LaWahini (mouse). Diamonds In The Desert reintroduces Clarice from the Chip N Dale cartoon "Two Chips and a Miss" who plays with the two 'munks, but who also is the crush of a mouse. It also introduces a third rat who looks a lot like Rat Capone and Francis (they're brothers in this 'verse), and who hits on Gadget a lot.
In Arad's Stardust, it's fairly common in Equestria, in part because there are an average of 3 stallions to every 7 mares. Upon hearing this, Lana immediately figures the best way get Twilight off the fact that she's XCOM's newest test subject is to imply that Matt thinks Twilight is cute. Twilight takes it very seriously, and even searches for information about "Human Courting Protocols." Matt is mostly upset how Lana refuses to stop teasing him about it, but there is some Ship Tease between the two.
Hinted at in Stargate Equestria between Daniel Jackson and Twilight Sparkle. Leads to the following exchange with O'Neill (which he quite understandably finds rather unsettling):
"If both participants are sapient beings, is it really besti —" "Do not finish that sentence, Jackson."
Superwomen of Eva 2: Lone Heir of Krypton: Asuka is half-kryptonian half-human and Shinji is human. Shinji really liked her and Asuka gradually fell in love with him due to Shinji being always there for her. Finally in chapter 19 they got together.
Lum Sum Purple revolves around Shampoo replacing Ataru in that fateful game of Tag, and ending up married to Lum. Also, Original Character Perfume (Shampoo's cousin) accidentally wakes up Kurama and becomes engaged to her, as well as developing feelings for Benten.
Love and Robots has Dinobot/Gem, as Grimlock falls in love with Garnet (only to learn that she's a fusion who isn't interested in adding a third to the relationship), then Jasper (who he marries, only to learn that she used to be married to Megatron).
The Bridge has Aria Blaze and Monster X as a subversion. While they are two very different species, both already two types of Hybrid Monster, they were both in human form when they met and had a majority of their interactions.
Zigzagged in The Wheel And The Butterfly Saga with Dan and Pinkie, sense Pinkie is technically stuck as a human when they first start dating, but played straight when she is turned back into a pony.
In A Charmed Life Light determines he needs to be closer to Ryuk to avoid the Shinigami getting bored and killing him. He becomes closer to Ryuk than anticipated when he discovers Ryuk has a crush on him.
In Death And His Shadow, L is a Psychopomp who wants to take Raito's soul after he dies... but when Raito doesn't die, he ends up falling in love with his would-be victim.
And The Story Continues has Erin and Umbra, a shinigami. Their relationship deconstructs the trope—although they do have genuine feelings for one another, Erin feels disgusted with herself and fears being rejected by what friends she still has because of the relationship. Plus their moral and cultural differences get in the way (for example, he sees nothing wrong with murder whereas she's an All-Loving Hero who believes Thou Shalt Not Kill). To further complicate matters, Umbra is actually L reincarnated after his deathin the prequel. Presumably the transformation is due to his usage of the notebook, and because she feels responsible for him, Erin can't find it in her to break away from him.
Subverted, however, with Misa and Lumen. Lumen likewise is Light's reincarnation, but not only does he still have no feelings for her—except condescending scorn—he doesn't even remember who she is. Misa, who still has feelings for Light and has been grieving for his death all along, definitively crosses the Despair Event Horizon upon figuring all this out.
All This Sh*t is Twice as Weird has Mahanon (Dalish elf) and Cassandra (human noblewoman). There's also, in the backstory of the setting, Darrian (Dalish elf) and Morrigan (human mage), as well as a couple of the pairings carried over from the source material.
The Vow is about the tragic love between Lord Shen (peacock) and Lady Lianne (swan). They have in the epilogue a child that's a peacock with some traits from a swan. There is also affection born between Zhan the Wolf Boss (wolf) and Jade (dhole).
Beyond Death has Thanos crash-land on Earth and meet a young woman, whom he temporarily moves in with. While he plans to kill her once he's recovered his strength (the only reason he doesn't is because she gets fused with the Tessarect), he ends up falling in love with her and vice-versa.
The Uplifted trilogy has Joachim Hoch and Hanala Jarva vas Devoas, an SS officer and Quarian Captain, and the affair between Erwin Rommel and Admiral Utala Falan. In the next series, it's revealed that although some mxed species couples try to make it work, few relationships last. Even the Jarva-Hoch family is strained with the difficulties of mixed species family, with John Hoch's newly discovered daughter flat out rejecting any kinship the quarian side of her father's family has. Which is understandable considering she is noted unrepentant quarian killing Commando Otto Skorzeny's Granddaughter and raised by an equally xenophobic mother
The sentient dinosaurs in Mesozoic Effect are firm believers in this, which is unsurprising considering the sheer number of sapient dinosaur species. Children from such parings are normally Designer Babies created by the dinosaurs' extremely advanced genetic engineering. When they awake from cryonic suspension, the dinosaurs see no particular reason why the humans who now control Earth wouldn't also make suitable mates. This eventually leads to several anatomically confusing pairings. For example, Ashley Williams' mother is revealed to be a Cetiosaurus, while her grandmother is a T-Rex. Both her father and grandfather are human. Careful reading reveals reference to Ashley's egg, suggesting that all this mixed parentage has had a serious impact on her eventual species.
Twi and Me has human male and female pony (Twilight Sparkle).
Xenophilia involves Rainbow Dash getting a human boyfriend. Despite being a Lemon the fic spends a fair amount of time discussing differences between humans and ponies as come to sex and gender relations. It mostly treats the human as the alien partner (talking about his Exotic Equipment, for instance).
The Mixed Up Life Of Brad has this between Brad the human, and Twilight the unicorn. Subverted a bit, as Brad fell in love with Twilight when she was transformed into a human, and now that she's back in her pony form he finds her physical appearance unappealing. It is noted that they cannot ever be truly happy together, being so different from each other.
The same author's A Mighty Demon Slayer Grooms Some Ponies gives Danny (from G1 My Little Pony), an eleven-year-old human, a crush on Surprise the pegasus (who is an adult at the time by pony standards). Nothing comes out of it, and he still has bad memories years later. It's hinted that it's all because he was still a young kid at the time, confused by his budding sexuality.
Mating Customs of Species Equus parvus explores this a bit: Humans have a tendency for seeking exotic partners, an evolutionary trait which used to help them reduce inbreeding by encouraging them to find partners in other communities. As a side-effect, it makes them prone to Interspecies Romance with other sapient races—which, however, do not share this trait, so such infatuations are pretty much always one-sided (and result in the unlucky human suitor laughed off).
Arddun Lleuad and its sequel, Chwe Goleadau, has the romance between the human protagonist and Luna as one of its main themes. They have some anguish over just how far are they going to take their relationship. At the very end, the point becomes moot, as the protagonist gets castrated by the villain.
In All-American Girl, there are close relations between Earth and Equestria, and pony-human relationships or couples are not unheard of—the protagonist herself is a pony married to a human. That said, the setting also has temporary species-transformation magic available for the spouses, allowing such couples to actually have children together.
In Equestrias First Human, a socially awkward teenager falls in love with Fluttershy. It is averted later on when his spirit is brought back to Equestria, he chooses to be reborn as a pony, since he could love Fluttershy more easily that way.
Averted in The Rise of Darth Vulcan. Due to changeling custom and instinct, since Vulcan beat Chrysalis in a fight, she becomes enamored with, and dedicated to him. Vulcan, however, is completely disgusted with both the concept of this trope, and Chrysalis herself. So, he uses her for information and experience, but refuses all her advances.
In Summer Days And Evening Flames, Gilda (a griffin) eventually starts dating her guard captain Iron Bulwark (a pony). She's justifiably worried that dating him could make others look down on him, considering his best friend is very racist to griffins.
Kalash93 wrote Racer And The Geek, which makes Zecora one of the protagonist's primary love interests, if not his main one, and Welcome to the Brothel and Relax, both about a pony soldier and a zebra sex worker. This is only a borderline example, however, as canon isn't really clear whether zebras are a separate species to unicorns, pegasi and earth ponies or just another ethnic group.
A pair of recurring background characters in Cadence In A Minor are a stallion/griffon couple, who are also soldiers on the opposite side of a tense border. Despite everything stacked against them, they make a pretty cute couple, all told.
The Reading Rainbowverse has the typical Gilda/pony romance... but mixes it up by having a cat crush on Gilda too. Not an anthropomorphic cat... a normal housecat.
Strife, the Draconequus of Natural Selection, is Happily Married to Mortis, the Alicorn of Death, and they have kids.
Anarchy, the Draconequus of Freedom and Rebellion, is married to Nightmare Legion, an Alicorn formed from millions of Shadows of Existence.
Dark World!Derpy has feelings for the Doctor, which is part of her motivation for wanting to destroy the Valeyard and force him to regenerate back into the Doctor. She succeeds and ends up marrying him after Nightmare Eclipse's defeat, though he's using a Fob Watch.
Celestia and Discord were once in love, but the latter's Sociopathy and sadism ended that.
Minuette and Captive Audience, as the former is actually a Time Lord. Though it's a bit ambiguous after Minuette destroys the Master if she's still one or not.
TD ends up in one with Cheerilee in the main continuity of The Non-Bronyverse. In the alternative-continuity AU story where he gets accidentally turned into an alicorn, he eventually strikes one up with Celestia.
Discussed Trope in Romance and the Fate of Equestria. Iron Will tries to take his friendship with Fluttershy to the next level; Fluttershy politely declines and later consults her friends as to their thoughts about interspecies dating. When they all view it as a non-issue, this leads Fluttershy to think she's bigoted for only being attracted to ponies. When it's further explained that this is because she wants to have children, Rainbow Dash labels her a "breeder", and assures her that it's perfectly normal.
Zestar Apple Flambe involves Spike and Apple Bloom falling in love with other, and having a child together.
Bride Of Discord centers around Fluttershy and Discord. It is also hinted, that Discord had unresolved feelings for Celestia.
There is also a major subplot between Spike,note Who like in canon, has a crush on Rarity that does not seem to be reciprocated Rarity, and Applejack of all ponies. Applejack and Spike end up together. This is Lamp Shaded, when Spike points out that Discord and Fluttershy aren't even the same species, only for Applejack to point out the hypocrisy.
The sequel also has one between Discord and Fluttershy's daughter Screwball and Mothball, who is a changeling.
Yet another sequel in the series, has one between Iron Will and a changeling named Bellatrix.
Another Gardevoir related fanfic. This one is about a boy growing up with a female Ralts. Due to some genetics, the Ralts, then Kirlia, becomes more and more human as she spends time with the boy and their relationships develops.
Subverted here. It opens with a great big monologue about human and pokemon being intimate — even having offspring — is supposedly very common. The titular character has had two inter-species relationships: One with Tera, a pelipper, the other with Henry, a human. Neither of which was intimate. Tera just wants to be a dad, while she Henry just gets a kick out of tricking people into thinking they're a couple.
Old West: The canonical example of Rango and Beans, with him being a chameleon and her being a desert iguana. While they're both lizards, their species are quite different. The main focus is on a similar example between Rattlesnake Jake and Grace Glossy, who are a rattlesnake and a glossy snake, respectively. Also, Grace used to have this kind of a relationship with the father of her son Teddy, Benjamin Hares, who's a gopher snake.
Bait and Switch has one between a couple of Mauve Shirts from the USS Bajor's security department, Ensign Kate McMillan (human female) and Lieutenant (JG) K'lak (Klingon male). They're stated to have been in an on-again, off-again relationship for the last couple of months, but decide to go exclusive in chapter nine.
In Red Fire, Red Planet Lieutenant Commander Brokosh, a Lethean mercenary, is Happily Married to Klingon noblewoman Ba'woV, daughter of N'Gara, of the House of Chel'toK, a Klingon. Brokosh signed with the Klingon Defense Force when their son was conceived, since Chel'toK is fairly impoverished.
From Bajor to the Black has Kanril Eleya, a Bajoran, date a human Starfleet Academy cadet exclusively for about a year, to the point of her starting to talk about Bajoran betrothal rituals. This ends badly when Jerrod Dalton is offered early graduation and skips town for the USS Planck in the middle of the night.
In one 4chan copypasta fic King Arthur in a Peggy Sue scenario decides that he's better off in making that squirrel (who actually loved him and he has Merlin change into a human form) his Queen instead of Guinevere.
The Sirens of Azeroth suggests that the many species of Azeroth don't have a huge amount of trouble with, at least, casual interspecies romance/intercourse, demonstrating among others a Dwarf/Draenei (seven-foot faun-like blue alien) relationship, a Troll/Blood elf lesbian couple with an open relationship, and a pair of tiny gnomes talking about how their favorite types of 'men' are Tauren (hugeminotaurs), though they could just be making that up.
Zootopia/0 (still in production) introduced one of its first characters, Hazel Dodge, as the skunk who contributed to the famous rug. Though neither describes their relationship as romantic, Nick does concede that they were "Close enough to let her shave my butt."
Nick: "Oh, um... (nervous grin) Did I mention there's also a fox butt-rug somewhere out there?"