Barley and Ravenpaw from Warrior Cats 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 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.
This troper sees Poolcloud and Nettlespot's relationship in "Yellowfang's Secret" as quite a bit of Les Yay.
Firestar/Graystripe (Oh so very, very much of it, the final chapter of Forest of Secrets being especially noteworthy), Firestar/Whitestorm (If I had for nickle every time Whitestorm stands up for Firestar, and we are told how much Firestar respects Whitestorm... I'd be rich.), 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.), and Lionblaze/Stormfur (It 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). As for one-sided, we have a bit of Fallen Leaves/Jayfeather ("I could not leave you here to walk alone, when you walked with me like a brother."), Kestrelflight/Jayfeather (Kestrelflight isn't particularly surprised to see Jayfeather in his dreams), and Purdy/Sol (Purdy stands up for Sol all the time, plus they lived alone together for a while)... Hmm... I still think I'm missing some...
This troper is convinced Hollyleaf was in love with both Cinderheart and Willowshine.
Leafpool has some Romantic Two Girl Friendships with Sorreltail, Mothwing, and Cody that can easily be seen as this. Mothwing also has massive amounts of Les Yay right back at Leafpool, as well as some with Willowshine and possibly even Leopardstar.
Hollypaw also has plenty of Les Yay moments with Willowshine and Cinderpaw.
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!'. 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.
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.