The final page of the final story in Volume 5 of Empowered shows the scantily-clad eponymous character giving the likewise scantily-clad Sister Spooky a big hug. She also appears to be stroking Spooky's hair.
Nico and Karolina from Runaways, especially in the first issue after Terry Moore's run ended. After a game of "truth or dare" leads to Karolina stealing a magic staff from a bunch of white supremacists. Nico tells her "You pretty much always amaze me" with the two of them staring at each other. When pressed on whether Karolina, Victor or Chase is the better kisser, she eventually snaps and admits "Karolina". This is despite that they never actually got beyond Almost Kiss... as far as we know. Oh, and it ends with her chiding the boys for being "such 'phobes" while she and K have Intertwined Fingers.
Runaways and Young Avengers both do this pretty often, but their Civil Warcrossover really went crazy with it. Tommy calls Nico hot, Nico calls Eli cute, and Victor calls Cassie an angel after she saves his life (he didn't think people actually did that). On top of that, the Tommy/Kate/Eli Love Triangle and the Vision's crush on Cassie are more apparent than ever.
Demon Knights does this relentlessly with Exoristos and Shining Knight.
Not even going over the amount of Ho Yay in Sam And Max, the titular duo is constantly a: being "mistaken" for a couple, or b: having a character trying to get them dating, or c: being told that they are destined to be together.
The Nightmare Arc might as well be called "Secret of My Excess, Part 2" for all the Spike X Rarity moments. For one thing, Spike brings the Fire Ruby, plus Spike is one of the only two characters who could cause a reaction on Nightmare Rarity (the other is her sister Sweetie Belle) and it's Spike who delivers the final line that releases Rarity from the Nightmare's grip. The last panel of the arc's final page also speaks volumes.
In Issue 9, Big Macintosh practically has to fend off all of his female admirers— Sweetcream Scoops (who has been stalking him for several issues), Bon Bon, Fleetfoot (who gets an entire splash page and an alternate cover featuring her marriage fantasy about him), and even Princess Luna practically throw themselves at him. Zecora also follows him around, although if she's actually interested in him, she's at least more subtle about it than the other girls.
In Kick-Ass, for better or for worse, a lot of the scenes between Kick-Ass and Hit-Girl are framed from an odd angle where it looks like one is kissing the other (the dialogue bubbles dispel the notion, but the imagery is there), in addition to the two being about as close as anyone in the comic can be. The very large age difference may put it into No Yay territory, but Hit-Girl being both more mature and more experienced may not, so it's a YMMV/perception thing.
Shinji And Warhammer 40 K predictably has Shinji/everyone teases, though Rei gets the largest chunk of moments in her favour. Asuka/Kaworu got a lot of teasing too (including kissing) before Kaworu revealed himself as an evil bastard.
Fate Stay Night: Ultimate Master has some ship tease between Ben and his Servant Avenger, very much in the same way as Shirou and Saber have in the original source material. Examples include both acting like a Battle Couple, Ben being clearly stunned by how beautiful she looks and Avenger insisting on sleeping in the same bed as him for better security measures.
In the BlazBlue fanfic based off Help Me Doctor Hazama called Disaster Piece Theatre, there is quite a lot with Ragna and Noel. It is also heavily implied that there would be a fanfic that would delve more into it.
In Forward, there are a number of scenes that tease River/Jayne. The author does, however, twist these around quite a bit, and one of the most tense moments between the two is ruined by a realization that psychic mind-manipulation was involved.
The writer has some fun with this. He is believed to be the first person to ship Fujiwara/Kuyou, and has since turned it into a Running Gag that the pairing is very much one-sided. Chapter 84 is devoted to the Anti-SOS Brigade and deliberately has a lot of moments where Kuyou is affectionate towards Fujiwara. Fujiwara, who regards Kuyou as an Abhorrent Admirer at best and a rapist at worst, promptly Breaks The Fourth Wall and implores the author to stop it.
He has also parodied the concept when Kyon becomes a pervert and starts propositioning every female character in the show, as well as some of the men. They all give him a slap in the face.
Imperfect Metamorphosis has no explicitly stated pairings whatsoever, but loves to drop hints regarding popular fandom pairings such as Marisa/Alice, Yukari/Yuyuko, Kaguya/Mokou, and Yuuka/Wriggle. There is also something developing between Rumia and Rin Satsuki, though what exactly is difficult to determine given the general Mind Screw nature of their relationship.
The Teenage Mutant Ninja Turtles stories written by FF.net author Zarius tease the fanon pairings of Donatello/Irma and Leonardo/Lotus, and tries it's luck at a unique pairing by hinting at April/Michelangelo.
Fallen King has Ryou and Tea, but in a twisted way as he uses it against her and her friends.
The Equestrian Wind Mage: While primarily shipping Luna and Vaati, with some side flirtation between Rarity and Maulgrim, readers have also picked up hints of attraction between Twilight and Nigellas (though Word Of God is that that last one was unintentional).
Film - Animated
Secret of the Wings Periwinkle asks Tinkerbell (speaking of Terrence) "So is he your boyfriend?" "Uuuuhhhhh", cut to next scene without finishing sentence.
Po and Tigress. It is said in the commentary for the first movie that Tigress is Po's favorite of the Furious Five, even though throughout most of the first film she's the one in the group who is the most vocal about her disdain for him. It takes until the end of the movie for her to respect him. In the sequel while not romantic, the two share a lot of moments. When Po describes how confused he is about his past, and how Tigress wouldn't get something like that, she suddenly hugs him, much to the shock of the other Furious Five, and tells him she does understand. She then tells him that she can't watch her friend die, and to stay with Masters Storming Ox and Croc for his own protection. She also seems to be the most distraught out of the Five when Po is hit by Shen's cannon. Later, when Po returns and is about to get hit by Lord Shen's cannon, she pushes him out of the way. In the wreckage of the cannon-burst Po finds Tigress drifting and holds her hand briefly before pushing her out of harms way. After Po defeats Shen, he hugs her, with Tigress initially frozen in shock before a smile grows on her face, while everyone else looks on in shock.
To a lesser extent, Crane and Mei Ling in Secrets of the Furious Five, where the feline Action Girl is so nice and loyal to the bird in the All of the Other Reindeer situation that many fans like to imagine them having a romantic relationship while they are at it.
Rise of the Guardians teases plenty of Jack x Tooth - especially their hug at the end, and the little bit where they just stare at each other before Baby Tooth interrupts.
There were a few moments teased between Dory and Marlin in Finding Nemo.
In the ending of Wreck-It Ralph Rancis Fluggerbutter is seen checking out Vanellope von Schweetz with interest several times after his memories, along with the other racers, have been restored and it's revealed that Vanellope was the true and real ruler of Sugar Rush. The animators went so far to write a book about it, called One Sweet Race, where Rancis, sick of losing and never winning a Sugar Rush cup, gets Vanellope to help him build a kart to win a race for once.
In The Secret Of NIMH heroine Mrs. Brisby and the Captain of the Guard, Justin, flirt a few times, but both have more important things on their minds (not to mention that Mrs. Brisby is the widow of one of Justin's old friends).
Mrs. Brisby:[looking directly at Justin] Beautiful! Justin:[blushes] Oh? Mrs. Brisby:[giggling] The lights!
NXT season 3 had two sets of male pros with female rookies. The first set Goldust and Aksana were given a storyline involving a Citizenship Marriage while the second set AJ Lee and Primo got a more subtle tease. One episode had them trying to find a private place for an unrevealed reason, AJ loved to celebrate winning matches by jumping on Primo's shoulders, when she was eliminated from NXT she broke down crying in his arms and they finally kissed on the last episode.
Similarly from the second season there was Layla and Kaval who also had an onscreen kiss.
Billy Gunn & Chuck Palumbo teased a gay relationship with each other, going so far as to declare each other "life partners" and showering each other with affection.
Stephanie McMahon and Kurt Angle were involved as Just Friends in a love triangle with Stephanie's husband Triple H. Steph was originally planned to leave Triple H for Angle, but Trips used his creative control to stop it.
Stephanie McMahon and Eric Bischoff initially were duelling General Managers of Raw and SmackDown in 2002 and got an onscreen kiss during a Big Lipped Alligator Moment of a Halloween party. There had always been a bit of friendly Foe Yay between them.
Trish and Lita were involved in some teasing with Christian & Chris Jericho that was ultimately revealed to be an example of The Bet. This lead to an 'intergender' feud between the two pairs, followed by a Heel-Face Turn for Jericho when Trish made her own Face-Heel Turn as Christian betrayed Jericho with her help.
Melina and John Morrison got a little tease during a backstage segment in 2010 obviously meant as a Mythology Gag to echo their off screen relationship. They had been an actual on screen couple years before but had been separated onto different brands and this quietly disappeared. So the segment was this trope at the time.
Melina and Alicia Fox actually kissed on TV. Ditto for William Regal and Zack Ryder, although that was meant as comedy.
Kaitlyn and Derrick Bateman's "friendship" on NXT was this at first but they quickly became an Official Couple.
Kaitlyn's done this quite a bit. She's had Dolph Ziggler, Cody Rhodes and Hornswoggle. Funnily enough, her BFF AJ locked lips with the last two as well, and AJ is with Dolph Ziggler as of December 2012.
LayCool were a lesbian couple for as much as PG television would allow. Getting each other matching necklaces, always hugging each other and attending Couples' Therapy. Then Michelle had to blow it all by saying they weren't a couple.
Billy Gunn and Chyna had this going on when the former returned in 2000 to console her after her break-up with Eddie Guerrero. In Kayfabe interviews he would describe Chyna as "absolutely gorgeous" and they were shown to be very close. However whenever asked they would insist they were Just Friends. It never amounted to anything other than a friendship, though the 2001 Royal Rumble did have a very couple-y moment between them when Chyna was getting wheeled out on a stretcher.
Maryse and The Miz frequently throughout 2009. Maryse however was clearly just being The Tease, hoping to manipulate him into helping her. Miz sunk the ship at Night of Champions and pretty much told her to go to hell. However in real life the ship is sailing just fine for both of them.
Avenue Q teases Rod and Nicky from as early as the fourth song ("If You Were Gay"). Unfortunately for Rod, Nicky doesn't return his feelings.
Wicked teases both Fiyero/Elphaba and Glinda/Elphaba from their first encounters - what with "What is this Feeling?" sounding like a love song (loathe and love aren't too far off), and Fiyero being just as much of a Deadpan Snarker to Elphaba as she is to him (that, and his lack of shock, disgust, or caring at the colour of her skin).