Though no interspecies couples appear in either Ice Age movie, Ellie is quicker to conclude that Manny is "part possum" than that she is not a possum at all. Manny is bemused and Crash and Eddy are dismissive ("You wish [you were part possum]"), but no real indication is made that such a thing is unheard of.
It's also interesting that when Eddy worries that they'll have to repopulate the Earth, Crash points out that if their group makes up the last of the living creatures, "everyone left is either a dude or [their] sister." No mention is made of the various species that make up the small group.
Scrat and Scratte, although superficially similar, probably aren't of the same species: she's a flying squirrel and he's not (and is surprised to discover she is one). Possibly the writers simply didn't know that flying and non-flying squirrels are only distantly related. Or they did it for the lulz like they did with everything else in the movies.
Judging by the fourth movie, one can make an argument that this is really a case of Bizarre Sexual Dimorphism since Scratlantis shows creatures that look like both Scrat and Scratte.
Mama T. rex and Sid the Sloth. They each try to raise the babies in their own way, Mama brings Sid into the warm cave for the night, and later risks her life to rescue him from Rudy the albino Baryonyx.
The fourth film shows Louis, a molehog, having a crush on Manny and Ellie's daughter, Peaches.
Shrek starts out with Shrek and Fiona as ogre and human, and even after she becomes an ogre, too, we've still got a donkey/dragon romance, complete with mutant babies!
Not to mention that, as revealed in Shrek 2, Fiona's own father is the original Frog Prince, which might explain her dual physical nature.
A rather painful aversion in Disney's The Sword in the Stone: Wart (Arthur) gets turned into a squirrel temporarily by Merlin's magic, and a big-eyed girl squirrel falls for him, instantly turning into a Stalker with a Crush. Though annoying, she is terribly upset when Wart turns back into a human, and he apologizes, "If you could only understand," while she, not comprehending a word, runs away and cries. The scene fades with the poor squirrel sobbing her little rodent heart out, which seems to be the (for kids!) movie's only commentary on romantic relationships.
Over the Hedge has Stella the skunk and Tiger the Persian cat, who conveniently has no sense of smell.
Megamind: Roxanne and Megamind eventually end up in a relationship together. Although nobody really makes a big deal of it, he is an alien. She was also rumored to have an affair with Metro Man, a Human Alien; (he is actually "not her type).
Kung Fu Panda seems to be going this direction with Po and Tigress judging from the second film.
The TV series also had a duck and a pig.
AND in the episode "Love Stings", we see the oddest pairing EVER: Mr.Pingx Scorpion, the villian
There's also a female goat that flirts with Po all the time.
And how could we forget to mention that episode "Bride of Po"? A Valentine's day episode where Po ends up (somehow!) getting married to a goat that can do kung fu (not the goat mentioned above). Needless to say, Tigress is not amused...
Not to mention Shifu (red panda) and Mei Ling (fox).
In Bee Movie, Barry, a bee, is clearly infatuated with Vanessa, a human florist. That being said, it's not clear if they're officially together at the end; if so, they're a Chastity Couple for fairly obvious reasons.
Although by the end of the film they're on more-or-less equal ground: Him, a mostly-human-robot, her, a mostly-robotic-human.
TRON: Legacy has an interesting example of this trope. While there's no sex and barely any kissing, it's quite clear that Sam Flynn (human) and Quorra (ISO) fell in love with each other in the second half of the film. What woke up Kevin from his meditation on the Solar Sailer? A conversation between the two about sunrises and Quorra's beauty.Kevin smiles, because they found love in the least likely place.
Things could actually go pretty well, since Quorra became flesh and blood at the end, thus being a sub-trope of Robo Ship has been averted. It was actually quite refreshing to see that in spite of all this, they kept things so subtle that they avoided what could have easily gotten the characters Strangled by the Red String. Since it was pretty obvious what the audience would be thinking by that point, the writers knew better than to throw it in their faces.
Cool World: "'Noids do not have sex with Doodles." But Holli Would if Holli Could... and Holli Does.
An secondary example comes from the cop Frank (Noid) who's girlfriend is Lonette (Doodle) a Cool World waitress. Because of the law they can't consummate the relationship, which causes them both no small amount of torment.
A subversion from Earth Girls Are Easy: as the alien Mac calmly takes off his clothes, preparing to have the human Valerie, she keeps rambling on, trying half-heartedly to talk herself out of doing it. At one point she says "Maybe we're not even compatible..." (glances over...) "...OK, we're compatible.."
Definitely present, albeit unconsummated and one-sided, in King Kong. Peter Jackson's remake made it more of a mutual platonic crush on both sides.
Tank Girl — Human/Mutant-kangaroo-that-was-formerly-a-dog.
Who Framed Roger Rabbit: Roger and Jessica, who is a Rabbit by marriage only. Also, it's pretty clear that Eddie Valiant wasn't expecting her to literally be playing patty-cake with Mr. Acme. Does human/toon romance count as this trope if the toon is human(oid)? There's also apparently at least one other instance which doesn't appear onscreen; Doom tells the weasels that they'll Die Laughing "just like your idiot hyena cousins".
In District 9, the government issues the false story that Wikus had sex with a Prawn as a way of explaining his Body Horror.
City of Angels has Seth (angel), and Maggie (human). It doesn't end well.
Men In Black II hinted at this between Kay (Tommy Lee Jones) and an alien princess sometime in the past. Jay fell hard for a woman who also turned out to be a Human Alien, although she left Earth before it got very far.
Interestingly, it's implied the said Human Alien was Kay's daughter with the aforementioned alien princess.
The core plotline of James Cameron's Avatar, with a human falling for an alien woman while manipulating a half-human, half-alien body, the title avatar.
Everything You Always Wanted to Know About Sex (But Were Afraid To Ask) had a romance between Gene Wilder and a sheep.
The Underworld franchise has two interspecies romances as major plot points, the first (chronologically) being between lycan Lucian and vampire Sonja (which produced a lycan-vampire hybrid that unfortunately never got to be born), the second being between vampire soldier Selene and vampire-lycan hybrid Michael (although his hybrid nature was brought about by mingling viruses, not through sexual reproduction; he was born human). Selene's falling for Michael also makes her an Example of Defecting for Love.
Interestingly enough, the Fantastic Racism in this franchise is fairly well explored and deconstructed, particularly considering that both vampires and lycans are essentially mutated humans (due to an inheritable blood disease). The fact that a hybrid between the two races results in a creature that has the power to annihilate them both if it so chooses becomes an - if not the - major revolving plot point for the series.
Howard the Duck features a romance between Howard (a male anthropomorphic duck from another dimension) and Beverly (a female human from what is supposed to be our world).
Played with in The Muppets Take Manhattan (apart from the traditional Kermit/Piggy Official Couple). Masterson Rat, waiting tables at a restaurant, asks Brooke Shields if she believes in Interspecies Dating. She doesn't make the situation any better with her reply of, "I've dated a few rats before, if that's what you mean."
The plot of What Planet Are You From? involves an advanced human-like alien played by Garry Shandling assigned to mate and impregnate a woman then bring the baby to his planet. His planet's people are emotionless, reproduce by cloning, and their erect penis makes a mechanical noise.
In Star Trek half-human, half-Vulcan Spock is in a relationship with human Uhura. And of course there's his parents.
In Kamen Rider Fourze & OOO: Movie War Megamax Gentarou Kisaragi, the aforementioned Fourze, falls in love with a alien substance known as SOLU that has taken up the form of high schooler Nadeshiko Misaki. And becomes a Kamen Rider, too, doubling as a Battle Couple!
In Alien: Resurrection, this is very disturbingly implied between Ripley and one of the Aliens, in a sequence late in the film which is shot as if it were a love scene. The studio wanted to cut the scene because of the implications, but Sigourney Weaver demanded it be kept in the film.
Zoo is a documentary about an interspecies romance that went horribly wrong.
The Deaths of Ian Stone Main Hero - Ian (surprising?) is in love with a human girl, but later finds out, that he himself is a strange half-ghostly entity that feeds on humans fear. It is heavily hinted (though without iron proof) that his love for the girl is what makes him capable of killing his otherwise immortal folk.