The ever-inseparable Sam and Max have had quite a few instances of this, in particular Max who "doesn't like girls". He prefers violence.
And, true to the fact that all Ho Yay is where you find it, Max is always surprised to be told this.
Telltale pokes fun at this sometimes, like when Sybil Pandemik ran a dating service and told Sam his soulmate was Max, as well as a few possible jokes you can get using the wedding cake and engagement ring on Max, with Sam thinking over proposing to Max in his head, before giving his characteristic "Nah".
Although, in Sybil's position, wouldn't you do everything you could to keep either of them from breeding?
Besides, Sam thinking over proposing to Max, and being told that they are soulmates, most of the Ho Yay in the series is subtile, although there is one pretty blatant instance. There's a boxing ball on the coatrack. Sam says he bought it because he hoped it would make Max hit him less. Max says this is the way he shows affection. It quickly turns into a very Ho Yay conversation; Sam asks Max if he could stop showing so much affection before 6 AM, and Max says he could never stop loving Sam.
In The Glazed McGuffin Affair, when Sam slaps a hysterical Max to calm him down, he responds by saying "Hit me again. I like it!" This would be a weird thing to say, even for Max, but if he actually sees violence as a form of affection, then he might just like that Sam's being "affectionate" with him.
In one episode, Sam and Max raise a baby alligator like a couple. If it means anything, Sam is a frequent crossdresser.
In Little Bigfoot, Max was in Sam's pants. It almost makes a little bit more sense in context, but not much.
They even have a "break-up" mini-episode in there.
And to top it all off:
"You know, at moments like these, Sam and I have a special way of showing how we feel about one another"
Also the duo's aversion to the opposite sex. The ships practically write themselves to the point where I'm not even sure that this qualifies as Heterosexual Life-Partners anymore.
In "Moai Better Blues," you see the following conversation when you examine the punching bag.
Sam: I got this punching bag so that Max would stop hitting me. So far, it hasn't worked.
Max: But violence is how I show affection!
Sam: Then could you stop loving me before 6AM?
Max: No way! I could never stop loving you, Sam!
The Bachelor party in What's New Beelzebub? For once the duo's reaction mirrored the player's exactly.
Also, from What's New Beelzebub?, Sam's comment about Sexy Demon Peepers:
Sam: I hate to admit it, but Peepers is kinda sexy.
Max: If you're into small guys with annoying voices, I guess.
A Crowning Moment of Ho Yay: Harry Moleman frisking Sam in "Bright Side of the Moon".
In "The Penal Zone", if Max is with you when you pick up the ring, he will confuse the situation for a proposal.
Max: Sam, this is all so sudden. I don't know what to say.
If you use the Ring with Max outside Mamma Bosco's Lab, you get a whole cutscene, parodying DeBeers Commercials, in which Sam thinks about actually giving the ring to Max, but eventually discards this with a 'nah'.
The mere fact that Sam actually seems to seriously consider it says it all.
Max apparently has a habit of coming up with creepy disaster scenarios that end with him eating Sam to survive. Sam is annoyed by this, so Max tells him to just "stop looking so damn tasty."
Also a Crowning Moment of Funny, "Beyond the Alley of the Dolls" has a potential future for Sam as a reenactment of the death scene from Romeo and Juliet. Max is Juliet.
As for other characters, there's the way Skun-ka'pe and Papierwaite's relationship is discussed. While their brief cooperation itself doesn't merit raising of eyebrows, everyone involved refers to the end of said cooperation as "dumping", and the two even disagree on which one of them did the dumping.
In the dress-up Mini-Game, possible costumes for the guys include wedding clothes (Sam as the groom and Max as the bride).
If you attempt to ride the Tunnel of Love while Max is trapped in the tank, Sam will refuse, saying it 'wouldn't be romantic without Max'.