Enemy Quest has this as the focus of the story. Main character Zack and other eligible humans were selected by the government to hold a cultural exchange with the Visitors, using dating as the setting.
Variation in Misfile. Ash and Rumisiel pretend to be this, which would be Angel/human. However, it's not a real relationship, as Ash only tells her dad the Rumisiel is her boyfriend as an explanation as to why he's living there. Also, none of the humans know he's an angel, except for Ash and Emily and a few others.
The central theme of Kevin & Kell, although the world of Domain doesn't treat species the same way: the general division is carnivore/herbivore/omnivore (wildcard?)/insectivore. Then again ... Lindesfarne/Fenton and Danielle/George involve former humans.
Here it comes ... El Goonish Shive. Tedd is a human and Grace is a... human/squirrel/alien/another alien -hybrid shapeshifter (she can look full-human, but he finds Shapeshifter Default Form more attractive). The demonic duck also claims to indulge in this quite often. One of Elliot/Ellen alternates was in a relationship with Half-Human Hybrid boy, though this one didn't work out well due to the alien psychophysiology.
Also note the Uryoms, who are ambisexual, can be attracted to anything thinking and reproduce with anything moving (regardless of species and sex of "DNA sources"), but not in a way as "fun" as the Asari.
It's not interspecies if Kate, Hollie and the rest of the cast honestly don't have a clue what species Gina is.
Ozy and Millie has very little of this in its past (both leads are revealed as pure descendants of their natural parents, although Ozy is adopted into another home). But then, Ozy's father (dragon) and Millie's mother (fox) get romantically involved, and are now getting married.
Las Lindas has a really good amount of interspecies romance. One such romance is Miles, who's a cat and Taffy, who's a rabbit.
The Webcomic Love and Tentacles by humon is about a relationship between the male human Tom and the female tentacle monster Frida. In-Universe, humans and tentacle monsters livining together is normal, but a relationship between the two species is rare and causes some odd problems for the protagonists.
The titular character of Mandy has the hots for her owner Jeremy, but obviously can't be open about it, so she resolves to showing it in her own subtle ways.
Tally Road leans on this trope very heavily, too- working the angle that for most of the cultures involved, this interspecies screwing is both perverse and fairly common. There's literally a cat-house on a wolf planet (or 'Nerre-house' on a 'Runge' planet) and one of the cat ladies argues against getting into kink clients, pointing out that they are not kinky so much as they are exotic and different in the 'Runge' context. Another feline, in a moment of frustration, sighs at being 'judged by shaggy animals', upsetting his wolf companion and giving a tip-off of the cats' unspoken attitudes towards other species.
Matoya and Bahamut the self-professed Dragon God-King from 8-Bit Theater (Witch/Dragon). This Squicks the Light Warriors greatly.
Last Res0rt features it as a trait of the Celeste to crossbreed between as many species as they can, creating a race that can only be detected by how many wings they happen to have. At least one Celeste's backstory apparently involves a Cult of personality centered around him and the many, many women he tricked into having his children. It's Squicky enough before you even throw in the fact that he's a rather large humanoid (albeit with some feline traits tossed in) and the women he brainwashed were all small, furry, feline-esque Talmi.
It's also worth mentioning that Jyrras's parents are a kangaroo and a kangaroo rat who met when an accident in the personal ads department got the K species section mixed up. Seriously.
Jyrras follows in his parents' footsteps by being attracted outside his species line. He has a homosexual crush on first Dan and then on Abel, both cat 'Cubi, and a "I'm not sure it's real, but I do like her" crush on Lorenda, who is a half-Demon cow. Unfortunately for him, none of them are really interested in him back: Dan is straight, Abel isasexual and Lorenda believes Jyrras is gay, not bi. To say nothing of her entry in the "dating sim" side-comic stating she likes "beefy" (as in: big, strong, muscled and hunky) guys, whereas Jyrras is small, weak and adorable.
Dan, a cat 'Cubi eventually falls in love with Matilda, who is a Mythos of unnamed breed and thusly resembles something like a three-eyed cobra-hooded Naga with six limbs in a roughly "tauric" configuration.
Dan's sister, Alexsi, falls in love with Pyroduck, who is a Dragon disguised as an Indeterminate Furry.
Schlock Mercenary plays with this with amorph regeneration and reproduction. It does not rhyme with "pentacle rex", amorphs seem to reproduce asexually and can just study someone's personality traits to produce offspring — they evolved out of memory banks.
At one point Elizabeth, a 820-kg gorilla-like alien, kidnaps a human, beats (probably just scares) important information out of him, keeps him prisoner and sends a vacation request to his boss to go on honeymoon. Everybody believes that, meaning the story isn't too far-fetched for the 31st century.
In The Inexplicable Adventures of Bob!, Bob first met Princess Voluptua and the jellyfish creature Ahem when they were trying to escape an unthinkable Arranged Marriage to one another. Bob's girlfriend Jean is currently convinced that Bob and Voluptua have feelings for one another, despite the fact that Voluptua's real form is a giant insect (although her assumed human form is, indeed, quite attractive).
Later, Riff explains it was only because when she was suddenly like a woman, he went on autopilot; under the indifferent surface, he has major issues with women and can't deal with most of them normally, but he still manages to get dates by looking cool (or something) and goes trough a lot of girlfriends.
This is also how Leono bred his wraith army. Aylee was the one to find this squicky.
While we've never seen him in an actual relationship, Bun-Bun (a rabbit) does show a sexual interest in human women. It's also debatable whether Kiki (a ferret) has romantic feelings for Bun-Bun, or if her affection for him is just part of her general Friend to All Living Things personality.
Terinu has the alien title character falling for Gwen, a human girl his own age. In a canon text story by the comic's author, a human girl also apparently has a long running affair and eventually becomes engaged to a vulpine.
The erotic webcomic Dreamwalk Journal is all about this. The planet Cyeatea is inhabited by numerous intelligent humanoid insect and arachnid species, all nude with exaggerated sexual characteristics including female Non-Mammal Mammaries. There's lots of sex between species (some of it in the form of ritual combat, eliminating the need for real warfare) and with a couple of visiting human women.
Fur Will Fly and Coming Up Violet have had more then a few interspecies (interracial?) romances, but interestingly enough, the only confirmed child resulting from such a union is a mouse(mom)/human(dad) hybird who has her mother's body, and her dad's mind.
The bartender in Corner Alley 13 is the result of an interspecies romance between an ogre and a mermaid.
Housepets! has Sabrina (cat) and Fido (dog), but cat/dog relationships seem to be generally disliked by the neighborhood animals.
Also, the one of the main characters, Peanut, has a crush on Grape, who is a cat.
While Fido's brother Joey has a rather weird relationship with a mouse named Squeak, as in he cosplays as a cat.
A lot of fans pair King and Sasha together, even though King is a human that was transformed into a dog.
And on that subject, King has also developed a major crush on Fox's cousin Bailey, who is of course also a dog.
In a Nodwick story, the protagonists are hired by the human (and very attractive) Queen Bartha to route the army of the orcish chieftain Kurg, who is threatening war on her kingdom. Eventually, however, Nodwick realizes (through a series of Sherlock Scans) that Kurg is actually courting Bartha, the war being a fabrication so they can marry. (Both knew their respective races would never approve of such a marriage unless it was part of a treaty to end a war.) When this is revealed, Bartha's brother remarks it as "17 flavors of disgusting", but she replies she just "digs brutish guys in leather".
From WTF Comics: Anna & Smoke, Solkan & Vexana, Niami & Ngreth, and, possibly, Straha & Maguna.
Benny, of Looking for Group, is often called a "halfbreed", suggesting that her parents were of different species. However, since she was born in prison, the circumstances of her conception may have had very little to do with an actual relationship between her parents and more to do with the less savory aspects of prison life. Benny, herself, was at one point in a relationship with Sayl, a human, and some fans have speculated that there may be a future relationship between her and Cale, an elf.
Benny's half breed status is confirmed in a dramatic reveal here.
In Stubble Trouble, most of the furry characters are in interspecies romances. A few of the characters like Rennon (fox/wolf), Ally (cat/fox), and Gynette (jackal/spider and demon) are hybrids from their respective parents. Rosie (a Rottweiler) and Jeremy (a human) are in a relationship.
Sabrina Online is a rare case when many of the characters are hybrids of interspecies romance to begin with; Zig Zag had a Siberian tiger grandparent, resulting in her signature stripes, Thomas Wolf is actually only half wolf, but it was his mother that was the non-wolf fox, so his name is. More recently, pure skunk Sabrina is in a relationship with pure raccoon R.C., plus at one time had a rabbit Stalker with a Crush. More confusing is the relationship between married couple Thomas Wolf and Amy Squirrel, who have a boy named Timothy Wolf-Squirrel (who is also a quarter fox, remember).
In an early arc on Fans!, Rumy falls in love with an alien that resembles a glowing square with two eyes (the aliens are nicknamed "Xenochicklets"). The Xenochicklet ultimately realizes that their species are incompatible.
Not quite - it's just that the Xenochicklets reproduce mentally. It turns out they only wanted her for her mind.
In The Whiteboard, there are Jake (skunk) and Pirta (snow leopard) as a couple and more recently Howie (wolf) and Kasi's mom (cheetah). Plus, most of Doc's blind dates weren't bears. The other pairings so far are within the same species or close species (two subspecies of fox, two species of lynx).
The titular character of The Kenny Chronicles is a fox with black and white catlike fur (apparently there was a wild party). Also most of his girlfriends that have been shown are either foxes or cats (not sure if either of those count), though one was also dating a dog.
It seems likely that Kenny's half-brother Patrick is also a hybrid of some kind (what species is blue?)
And now Kenny's dating as of the last comic married to a lemming, whose parents are baboons.
Harkovast devotes an entire page to explaining the various implications of the various races forming romantic relationships.
The entire plot of Twokinds is built around this trope.
In Teh Gladiators, a Wo W webcomic, a murloc named Yolanda develops a crush on the human Vallant, which is most definitely not reciprocated. It doesn't stop her from smothering him with affection, going berserk when he's hurt, or sparing his life after he's captured by the Lich King (something that turns out very poorly for the latter).
The most noteable being the fact Kieri's entire families' stance on demons is to kill them on sight, no matter how evil they are or if they're children.
There is also the Mixlings, or "Bitza" (as the in-universe slang calls them), which are basically crossbreeds between two Median species. One character specifically, Toby, is a Hukai (or Jakkai/Human crossbreed).
Style Wager uses this a lot, both in his PG rated comic Dela The Hooda and his more pornographic stuff. Dela, an anthropomorphic fox (a "Hooda"), is dating a human and has stated that some members of her species can interbreed with humans (and she has the gene).
Elsseran (a fairy) and Corinn (a human) eloped, running to another world to hide and have kids. Corinn's brother Joralan went to find them, wound up meeting Lettie, and brought her back home as a bride. Fast forward to A Magical Roommate...
Before the revision it was stated outright in Fuzzy Things that attraction to other species was equivalent to homosexuality, it is yet unclear if that was retained. Note though, that most of the original cast are paired with an opposite sex member of another species (granted they are 8 years old), but among the second generation cast (12 year olds) there is one Official Couple that are both foxes.
Which is intentionally hypocritical, since he used to have a Foe Yay crush on John.
And Karkat's latest conversation with Jade alternates between him kissing up to her and him flaming her (and him flaming himself), right after he told the human boys to stay away from the troll girls, which Dave lampshades.
Furthermore, ever since the timeline was retconned, Karkat has actually been in a relationship with Dave. He could get away with this on the fact that this is a new timeline with an altered history, but it's still nevertheless hypocritical.
Eridan also has blackrom feelings for Rose, who is pretty definitively uninterested. When he continued his hate-flirtation after she said no, she blew up his computer. (Which might actually come across as a romantic gesture from the trolls' perspective, since one of their major types of romance is based on passionately hating each other. Humans do not work that way.)
Tavros also had a crush on Jade for a little while. It didn't work out.
Davesprite and Jade.
There has been some mild Ship Tease between Caliborn and Calliope and the alpha kids, particularly Caliborn towards Dirk, for whom he drew fanart of the two of them doing something 'more than friendly'. Considering that Caliborn is essentially a sociopath, any feelings are very vehemently unrequited.
As of Openbound, Rose and Kanaya are couple. Dave and Terezi were also confirmed canon at this time, but have since broke up.
Almost all of the romance among the secondary characters in Problem Sleuth falls under this. A few of the pairings are Fiesta Ace Dick and the Demimonde Semigoddess, the Higgs Bozo and the whale, and the Weasel King's marriage to Madame Murel, not to mention Pickle Inspector's homoerotic attraction to his fan.
Josh asked Frog Raccoon Strawberry to go out with him once, but she said that it would be too weird because he's a raccoon and she's a raccoon in a frog costume frog. Later, she ditches the frog costume and goes to see Josh, only to find him in a real interspecies romance with Pippi.
In Concession, Word of God is that species segregation has only recently officially stopped, but the cast seem to be making up for lost time, e.g. the Official Couple are a wolf and a cat, and other relationships include lemur/dinosaur, zebra/fox, and pangolin/skunk - even a briefly-appearing human customer with a guinea pig girlfriend. It's mentioned that the "Church of Gaia" are looked down upon for their advocation of sex between furries and non-anthropomorphic animals. Thonnen, the last of an important bloodline of African dinosaurs, intentionally dates outside her species to annoy her family.
Wales/New Zealand in Scandinavia and the World. Sure, they're both countries, but here's the thing. Wales, like most of the countries, is human. New Zealand is a sheep. They even have a child together, New South Wales.
While Sequential Art doesn't have an "official" interspecies pairing, the subject doesn't seem terribly unheard of in-universe. There's no inkling of taboo about the possibility when Kat's old college friend mistakes her and Art for a couple (and Kat later admits that she does find Art attractive).
Dmitri pretty much sleeps his way through the galaxy. The closest he comes to a mutual romance is either with Dal, who betrays him, or Haldeyis, who gradually loses interest when Dmitri becomes immersed in his job as Apex Speaker.
Curn (a slimy, betentacled thing) and Oohlooh (a small, birdlike creatures). In this case, they're biologically incompatible—neither can breathe the atmosphere of the other's homeworld, and one or both of them would die if they touched each other.
Pierrot (human) is courted by a Qiyemp female. It doesn't work between them.
After Martina is driven into hiding, she moves in with the hermit grub-alien Luunock who is murdered in an attempt to capture Martina. Nogg has to do some hasty back-pedaling when he realizes Martina's father doesn't want to hear exactly how close they were.
Reptilian hitman Growp finds his mutual enmity with Emily becoming a crush, and takes a laser for her.
Drowtales references the idea with a male drow called Val'Doom who has a harem of human women that he tries to make babies with, even though fae and humans aren't capable of reproducing. This gets compared to bestiality since humans to drow are held to the same standard as chimpanzees are with humans.
A notable subversion occurs with Mel'arnach and Zhor, a giant spider, who are often called this, but Zhor is in fact a dark elf who was transformed into a spider, and as a result his children including Ariel are full-blooded fae.
21st Century Fox has a bat and a mouse in a romantic relationship and even discussing how they can have children when they're not genetically compatible.
Bittersweet Candy Bowl has a number. Notably, in this universe, such pairings can NEVER create offspring. This means that cats and dogs can sleep around with each other a lot without worrying about unwanted babies (something Rachel takes advantage of), but it also means that if they DO fall in love, they can never have biological children (ironically, a problem for the same character, because she wants to have kids someday).
Abbey's foster parents.
As a small set of examples, Katie has flirted with Mike, Paulo has had flings with girl dogs (particularly Rachel), and David hits on Lucy a lot. Oh, and David may have a thing for Mike earlier and Abbey now.
Since Eerie Cuties is set at an All-Ghouls School hosting a variety of humanoid beings, this was practically a given and has featured two relationships between varying monster types:
For starters, there's Layla's (a vampire) on-again/off-again relationship with Kade Whiteclaw, who's a werecat.
And Ace's (werewolf) relationship with Brooke (a melusine), who have alsodated and broken up several times.
In its Spin-Off series, Magick Chicks, Cerise (a witch) briefly pretended to date Callista (a human), in order to gain popularity. While her former friend and fellow witch, Jacqui, has been seing Faith's brother, Paul (a human), and using a glamour spell to date Mr. Delatorre (a human magic instructor) at the same time.
There are several in Guilded Age. Byron the human and Syr'Nj the wood elf are the first confirmed couple, and later Syr'Nj's sister Fr'Nj starts a relationship with Scipio, another human. On the other side of the comic's conflict, there's Harky the troll and Gondolessa the avian.
Oglaf: Just... wow. The sheer absurdity of some combinations is mind-blowing. Just as an example, a reoccurring character is the concept of metaphor, expressed as a giraffe with dozens of millipede-like legs, pretending to be various household items in order to seduce a male human. Yeah.
Endtown might have this all over the place, depending on how you look at it. After the apocalypse, much of the world was mutated into anthropomorphic animals, so while they were originally human, they have the appearance of different species, and since the animal to which you mutate is random, the odds of hooking up with someone of the same 'species' are actually somewhat slim. The two main pairings in the comic are between a non-mutated human and a rhino mutant, and a cat and mouse mutant.