Arguably, the three other penguins for Skipper; the line between it and their general admiration for him is thin. Like the episode where Skipper "died" and Rico hacked up a framed photo of Skipper to "Why? WHY?!?" over. Or Private trying to get Kowalski and Rico to smack him the way Skipper does, "Like you're disappointed, but you still care." Or Kowalski's D= whenever Skipper chastises him/skips Kowalski as The Idea Guy. It works in reverse too. In "Needle Point," Skipper performs a seductive dance in a desperate attempt to distract the other three penguins and therefore not get his shot. This leads you to wonder why the HELL he would think this would work.
In one scene in the episode "Tagged," Private tries to get the others to act like real penguins:
Skipper: (beak-to-beak with Rico, clearly uncomfortable) Is this... really necessary?
Private: (checks book) Yes, it's critical to maintaining social order. You preen Rico first, then he'll do you!
Just before it seems Skipper must groom Rico, Kowalski interrupts them and Skipper slaps Rico away and onto his back. Later in that same episode, when Private and Skipper are wrestling, we get this:
Scientist: Male penguins now exhibiting bizarre mating dance ritual.
As soon as Skipper hears this, he knocks Private off him in a hurry. This happens again, in another episode, where Private and Skipper are fighting over Macguffium. Only this time, the commentary is from Julien:
Julien: Aw look at them Maurice. Why can't we play affectionately like that?
In Street Smarts Rico sniffs Skipper's butt. Skipper tells him to "Down, boy!"
Mort's Yandere-like obsession with King Julien, and King Julien's feet in particular. After the butt-scratching scene in "Field Tripped," the writers aren't even trying to keep Mort's obsession with Julien subtle at all.
Also present between Mason and Phil, particularly Mason to Phil. "You dog." Mason referred to Phil as his partner, too. Without any sort of business situation.
"Kaboom and Kabust" was markedly un-subtle in creating a Rico/Julien pairing, with both parties being very touchy-feely toward the other. There's also this line of dialogue from Julien: "You know, I could think of a many other things that could use a good... kabooming... if you know what I mean." Looks like the writers aren't even trying to be subtle anymore. They held hands as they frolicked through the park, and ate a snowcone together. Julien gets Rico's name right. They hug, and Mort squeezes himself in between their hug. Rico glomps Julien when the other penguins try to take him away. As a bonus, at the end of the episode, Julien and Maurice walk off arm-in-arm.
For that matter, Skipper carries Rico away over his shoulder and isn't even bothered by his rank insubordination in the episode. Right before this, when Rico falls unconscious and starts dreaming, the other Penguins essentially swoon over him in his sleep, but in that instance they treat him more like a pet than anything.
Rico seems to be properly gay. His Miss Perky doll vanished midway through season 1. He also seems to have more Ambiguously Gay moments and no show of interest in females, even as a joke. It's certainly more original because Rico is an unabashed Tough Guy, and people tend to associate homosexuality with the femininity shown by King Julien.
In one episode, Julien returns to his habitat and greets the other two lemurs with "Honeys, I'm home!"
Skipper: And by the time this is over, I'll have four sweet, sweet words for you.
Julien: Ohhh, "I love King Julien"?
Skipper: Yeah! N-No!!
Also between Skipper and Dr. Blowhole himself, quite possibly; at least, one-sided. This is kinda default for Nemeses, though. Dr. Blowhole mistook Julien for Skipper's BFF and kidnapped him. The fact that the Damsel in Distress usually hooks up with the hero makes this more Ho Yay and Foe Yay. Speaking of Julien being mistaken for Skipper's BFF, the other penguins tease him about Julien. Cue Skipper telling them that "He's not my BFF!" Julien kind of gets all over Dr. Blowhole, too. He gets out of his cage, doesn't try to escape the lair, rubs himself all over Blowhole's 'pleasant to the touch' skin and tells him he's got a proposal for him; "Not the marriage kind of proposal, uh, a different kind." (with a wink). Julien also doesn't mind doing things for him (like hefting the dolphin off the floor by himself), when normally he'd be outraged if anyone asked him to do anything. Blowhole doesn't mind, either, even smiling and warming up to Julien after he compliments his skin and makes him his partner. Of course Julien was a double agent and everything, but still...
Hans enjoyed heckling Skipper WAY too much... The card he made for him had hearts on it. And the whole "Palsy walsys" line didn't help. Plus, dude brought Skipper pastries. And we never did find out what happened in Denmark... Except that it happened in Copenhagen, involved fish, and Hans kissed Skipper's sister, who does not exist. (in the Spanish dub, Skipper points out that he has a brother, not a sister.)
To add more ambiguity to the matter, there's an episode that points out that there is almost no way to tell if a penguin is male or female, and if said penguin he kissed had enough resemblance to Skipper that he thought it was Skipper's nonexistent sister...
Let's be clear here, the card that Hans made had hearts on it yes, but it was above a crudely drawn picture of the two of them hugging.
How about we just agree that everybody likes Skipper? Everyone seems to have the general consensus that Private's extremely cute as well (including Julien).
Private: Sorry Skipper; I'm not feeling very cute or cuddly today.
Kowalski: Oh, stop. You're always cute and cuddly and you know it.
In The Lost Treasure of the Golden Squirrel Julien's deepest desire was living with Maurice and Mort, which he was doing already. Aww... Shown again in "All King, No Kingdom", when Julien starts to Go Mad from the Isolation when Maurice and Mort leave him. Private seems to get the vibe as well:
"He needs you, Maurice. More than you ever knew."
Meanwhile, Maurice's wish was for an "army of Julien manservants".
Julien's enthusiasm about being "pampered" in "Two Feet High and Rising":
In "Go Fish", Julien actually kissed Mort, who was disturbingly happy about it. Julien then realized what he'd done and was horrified: "See, Mort? I am so happy I forgot for a second how disgusting you are!" Mort remained happy. And in "Lemur See, Lemur Do" ... well, does it count as Ho Yay if it's with a robot version of himself? Mort being jealous of the robot is a pretty obvious case, though. In "Paternal Egg-stinct", Julien was disgusted to find out where mammal babies come from, and then there's the time he demanded of Maurice "Scratch me here until the tinglies go away!" (He was referring to his armpit, but...)
Julien to Maurice in Friend-in-a-Box:
"Uhh, say, Maurice...have you ever noticed my...southern extremities?" (eyebrow wiggle)
Private's hero-worship of The Archer and his disappointment when finding out Archie's real Jerk Ass nature has hints. "Even your charming French accent was a lie!"
In Driven the the Brink, Skipper and Private get a newspaper blown in their face so that their heads poke through a picture with the headline "Just Married!" Interestingly though, Skipper was the bride. Same episode, Julien seems to let Mort cuddle his tail while they're in bed with Maurice.
Skipper was going to leave Leonard the koala in the middle of the city asking "What's the downside to leaving him again?" until he realized the downside was that that would make Private sad.
Can't Touch This has Mort saying "See? King Julien loves meee..!" when Julien doesn't want the penguins to borrow him...but then he promptly shoves Mort over to them saying they should keep him forever instead. Mort doesn't care and persists, saying "That was a love shove." In Sting Operation, Mort wants to get the "bees'" honey because "I need it for King Julien to love me!". In "The Otter Woman", Julien and Skipper both fall obsessively in love with "Arlene", who is really Marlene with bleached fur, and in the final shot we see Mort with bleached fur, happily calling "Oh, King Juuu-lien!"
The episode "Right-Hand Man" features the new arrival Clemson effectively seducing his way into Julien's good graces, including rubbing his back, scratching his butt, allowing Julien to use him as a footstool, and actually being allowed to touch Julien's feet. Shame he turned out to be The Starscream.
In "All Tied Up With a Boa", Kowalski readily says that Skipper's "musk" is "intoxicating" (though this was said after misunderstanding the order to "butter up" Skipper).
In the preview for 'Pet Peeved' Kowalski yells "I love you" to Skipper as he's being taken away.
This isn't even handwaved or explained away in the actual episode, where he really does say it as Skipper is being taken away.
In "Blowhole Strikes Back", Rico is incredibly upset while Skipper is away, and can barely sleep until he is "ordered" to by King Julien pretending to be Skipper.
"Time Out" ships Kowalski and Julien after a malfunction in one of Kowalski's inventions causes everyone except them to freeze in time. Julien gets excited at the fact they can do anything they want and does a Over-the-Shoulder Carry on Kowalski. They end up becoming friends during a musical number with them actually having a good time and even spray painted an image of them with their arms thrown over each other's back smiling. After everything goes back to normal it ends with them giving each other and chewing bubblegum.
When everything goes back to normal a happy Kowalski holds Private up high and asks him to say something "naive but adorable".
In "Operation Break-Speare", Kowalski blasts penguin mating calls at the lemurs, full volume, in order to combat their music. This doesn't work as intended...though the effects are long lasting, apparently.
Rico:(getting real close to Kowalski) How you doing?
In "The Falcon and the Snow Job", there's an amusing scene where Skipper and Kitka exchange suggestive eyebrow gestures (well, whatever birds have for eyebrows). Rico takes it as a cue to do the same to Kowalski.
The unaired episode "Best Foes" which you can find online has arguably the most Ho Yay in the entire series. Skipper is zapped with Kowalski's invention which causes him to view his friends as enemies and his enemies as friends. This means he sees the other Penguins as his enemies, while Hans the Puffin and King Julien are seen as his friends. Basically, it breaks down into what can only be described as two jealous lovers fighting over Skipper. The words "I love you" are even said at one point!
Hans accidentally admits his secret dream of being Skipper's bestie, Julien possesses a framed photo of Skipper dressed as a cowboy (and is crushed to learn that Skipper usually dislikes him), and Private laments the fact that Skipper never took wacky photos with him.
Skipper seems to fondly remember the time he forced Rico to suck cobra venom out of his left buttock in "Roger Dodger", which horrifies Roger, Kowalski and Private.
In "Mort Unbound" there's a brief shot of Maurice feeding Julien grapes with a rather seductive expression.
Fred apparently lives with a Spanish guitar playing otter named Antonio.
Rico and Kowalski seem to get the most subtext between the two of them, probably because they're seen interacting the most out of the penguins and because Rico takes his cues how to be around Kowalski from mating calls and flirting of others.
In I Know Why The Caged Bird Goes Insane Skipper calls Kowalski baby and lets himself be convinced to go to a science fair through Kowalski's puppy eyes. Skipper. At a science fair. Egads!