Berserk, in both the manga and the anime adaptation. Oh my god, I don't even know where to begin with this one. Griffith's penchant for declaiming long, soulful speeches to Guts while completely naked for no real reason is probably a good place to start. Or just relies on the phrase, "Naked water fight." Not to mention how he frequently reminds Guts, "You are mine." The whole battle between him and Guts before Guts left has Griffith acting like he was being jilted by his lover, and reacting like a possessive Yandere about it. In fact, during Griffith's Ho Yay-tastic fight with Guts before Guts left the Band of the Hawks, Griffith is shown having thoughts of If I Can't Have You towards Guts. He considers all the different possibilities of attacking Guts, realizing that one way, if executed properly, would most likely end in Guts' death. He hesitates, but then thinks to himself, "But... if I can't keep him here..." and ends up attempting it. Of course, he fails. And then there's how his Heroic BSOD was caused by Guts leaving him, resulting in him acting irrationally, and what looks like him rebounding by sleeping with Princess Charlotte.
Pre-Eclipse Griffith grows green with envy when he notices that Guts and Casca have become an item, Kubrick Stare and all. It is unclear who he envies more due to his ambiguous sexual orientation. It's possibly both.
Don't forget that even before that, Casca was really jealous of the attention that Guts got from Griffith because she was in love with Griffith.
Or how Guts during their first fight says that Griffith has a "pretty face".
Or how Guts simply could not stop staring at a naked Griffith when he was giving him his soulful speech.
What's not quite so clear cut is whether Guts reciprocates Griffith's feelings. Though given Guts is (admittedly) obsessed with him.
Though after the Eclipse, shipping these two would count as Foe Yay as well as Ho Yay.
Berserk was inspired, in part, by the western film Lady Hawke, in which two lovers are kept apart by their respective transformations. A woman into a hawk by day; a man into a wolf by night. Hawk and wolf (or wolf-like beast). Two lovers. Hm.
Don't forget that Guts thought Griffith was gay when they first met, which lead to Guts telling him that "if you can beat me I'll be your soldier, your lover, whatever you want."
That's one of those lines that's translated differently in just about every version. "Lover" is about as tame as I've seen it. It's more commonly translated as "fag boy."
The more Squicky bit of Ho Yay has to be when Griffith comments on his many, many conflicting feelings for Guts, moments before sacrificing his men to the Godhand, turning into a demon, and then raping Casca, his love interest, which was all most likely done purely out of spite. And the entire time he's doing that last bit, he has Guts held down by some demons so he's forced to watch and his eyes never leave Guts's face.
And then there's when Guts and the Hawks discover Griffith broken and tortured body, Guts cries while holding him and then goes... well, berserk all over the Midland guards holding Griffith captive, killing them in great swaths.
It's especially interesting to note that Guts Hates Being Touched except by his Love Interest Casca, and yet he didn't seem to mind when Griffith held his face in his hands, got really close following their first duel, looked into his eyes, and said "You belong to me now, Guts."
If you go by Freudian imagery there's also the part during their first fight where Guts put Griffith's sword in his mouth.
Also, Griffith trusted Guts with the seedier elements of his power plays and opened up to him more than anyone, even Casca.
Adding to the tension between Guts and Griffith is what happened after the Eclipse, when Griffith comes back to create his new army and build his kingdom on earth. The first thing he does is encounter Guts at the Band of the Hawk burial. He tells Guts that he just wanted see if feelings once again surfaced in his presence, and was happy that they no longer did.
And then there's the manga-only scene in the library where Griffith is reading what appears to be the Kama Sutra and offers to lend it to Guts.
There's also Rosine, the "Elf Queen" and Jill, two minor characters in a story arc shortly after the Eclipse. Also counts as Squick given the age of the two.
Berserk does have quite a bit of Les Yay, such as between the Luca and another prostitute. And Casca and Farnese as well.
Some of the first glimpses of Farnese's Character Development are based on her relationship with Casca and how she grows to learn how to try to take care of someone else. She gets pretty protective over her and when she temporarily leaves the group, Farnese constantly thinks and worries about Casca, rather than Guts whom she had developed feelings for and was bedridden with injuries at the time.
Post-Eclipse Casca gets a few bathing scenes. Cue in the Les Yay with either Farnese or Schierke.
Pre-Eclipse, when the Hawks parade to the castle after winning the final battle of the war, lots of women in the crowd Squee over the warriors. Including (or especially, seeing as how she's the only one they're seen mentioning by name) Casca.
Many guys in the series tend to find Griffith attractive.