Barley and Ravenpaw are two toms that live together in an abandoned barn, having little interaction with other cats. When they do see other cats, they act like a married couple. The amount of Ho Yay between them can get pretty surprising, considering it's a series for pre-teens about talking cats. Even fans that hate male/male pairings ship these two, or at least recognize the possibility. That's saying something.
It's also worth noting that the author once said that she envisions Ravenpaw and Barley like a married couple. And once remarked that they are perfectly happy without any girls to boss them around. Yeah.
Darkstripe's idolization of Tigerstar would probably count as well. He literally follows Tigerstar to the grave, and the one time he refuses to go with him, right after Tigerstar's betrayal of ThunderClan, it's because he was jealous of the fact that Tigerstar was sharing his plans with Brokentail instead of himself, Darkstripe.
Poolcloud and Nettlespot's relationship in "Yellowfang's Secret" contains quite a bit of Les Yay.
Firestar/Graystripe; there is so very, very much of it, the final chapter of Forest of Secrets being especially noteworthy
Firestar/Whitestorm, as Whitestorm constantly stands up for Firestar, and we are often told how much Firestar respects Whitestorm.
Brambleclaw/Hawkfrost. Brambleclaw jeopardizes his relationship with Squirrelflight because he spends too much time with Hawkfrost. And then when things get patched up between them, he still meets Hawkfrost in secret.
Lionblaze/Stormfur, which starts with Lionblaze thinking that he likes Stormfur, and then eventually culminates with a Jayfeather detecting a rush of warmth and a strong bond between them.
Fallen Leaves/Jayfeather ("I could not leave you here to walk alone, when you walked with me like a brother.")
Hilariously, the authors have said that the only "serious" topics they won't cover, because "they won't fit into the Warriors world very well," are drugs and...homosexual relationships. Uh, guys, I hate to break it to you, but...
What the authors meant, probably, was that they wouldn't write Gayngst or get tied up in plotlines like 'Oh, I love him! But he's a tom! How can this be!'. As shown by Kate Cary's recent confirmation of Tallstar/Jake as canon, they're fine with portraying homosexual relationships, but they don't want to use homosexuality as a source of drama or discuss it in canon.
Well when someone asked Vicky outright on her facebook if Jake and Tallstar were together, she mentioned something about how there are certain things you just can't do in kids' literature in this day and age, and also basically said "I can neither confirm nor deny". Which makes it seem like yes, they are a couple, and the reason it isn't more overt is that Executive Meddling will always get in the way of canon gay relationships.
Blossomfall gets a lot with both Ivypool and Dovewing. This is especially notable in Sign of the Moon seeing the excitement she displays when Dovewing becomes a warrior (because now they can spend more time together) and when she and Ivypool go on a walk in the tunnels.
Shrewtooth and Sharpclaw from SkyClan. Shrewtooth's constant drive to please Sharpclaw can be read as love.
Tallstar and Jake in Tallstar's Revenge. They have a lot of physical contact, especially considering that platonic friends touch a lot less in recent books, Talltail loves Jake's son as if he were his own, and when he receives his nine lives, Tallstar even says that he loves Jake.
It helps that one of the Erins has stated that Tallstar never took a mate or had kits and that when he dies Jake is the one to guide him to StarClan when with most other cats it's a mate or family member.
Not to mention that one of the Erins stated that the reason Tallstar never took a mate was because "his heart always belonged to his Jake."