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 the fact 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 has been doing 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 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.
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.