More prevalent in the novels?! Did you miss the shot in the RotK film where Sam helps Frodo to his feet on Mount Doom by grasping him by the hips from behind? On top of that (not the happiest of phrases perhaps) the great reunion after the ring is destroyed (the child in me would like to note that the innuendo here writes itself) where Merry and Pippin's first instinct on seeing their friend is awake is to climb into bed with him under the gleeful eyes of a maniacally laughing Ian McKellen!
In fact, when Sam is battling Shelob to save Frodo, Tolkien specifically describes him as having the ferocity of a wild animal defending its mate.
And don't forget: the author also wrote that Sam tenderly took Frodo's hand and blushed.
On top of all this, Sam has to go rescue Frodo from the Orcs' tower... and Frodo is nude when Sam eventually finds him.
For this troper, the Crowning Moment of Ho Yay in the books is when Gollum comes sneaking up and finds Sam, asleep, with the also-asleep Frodo's head in his lap. As if that weren't enough, there's also plenty of Purple Prose about the fact that Sam's cradling Frodo's face. Even for the most physically demonstrative platonic friendship, that's way over the line. Heck, if Frodo had been dying, face-cradling would still be a bit much.
Ah, and let's not forget Sam constantly referring to Frodo as "my dear". And how Sam occasionally kisses Frodo on the forehead or hand in the book.
Since almost all of the characters are men, some can find Ho Yay all over the place. It was even mentioned in Lord of the Fans.
Not to mention the "great love that grew between Gimli and Legolas", quote from Return of the King. They warm up to each other during the course of the books, then travel to Middle-Earth together and end up sharing a boat bound for Valinor. Heterosexual Life-Partners at the very least.
Sure, it's Legolas and Gimli in the novels. But the love belongs more to Legolas and Aragorn in the films.
There's a scene in Two Towers where Legolas returns the Evenstar to Aragorn after he returns from his fall off the cliff. Meanwhile, Éowyn looks on from a distance, shocked, apparently under the impression that Legolas and Aragorn are romantically involved. The intensity of eye contact and gratuitous touching doesn't really make a case against her assumption.
Oh, and let's not forget how Sméagol addressed Déagol as my love, and how Déagol mentioned giving Sméagol "more than he could" on his birthday.
Not to mention Pippin and Merry. Yeah, they're cousins, but IIRC Merry's wife Estella was also his cousin. Pippin also married, but that doesn't stop the fans from seeing Ho Yay. After all, the two tend to stay as close together as possible, when they are separated it's like some sort of tragedy, and after the war they not only buy a house together and stay there for as long as they can, they also left the Shire together to go off and die with the humans, leaving wives and children behind. Although it's notable that while Merry and Pippin are joined at the hip from their first second on-screen in the movies, in the books the closeness isn't apparent until later. In fact, it's actually Merry and Frodo who seem to be the bestest buds in Fellowship, and if IIRC Merry even lived with Frodo for a while after Bilbo left.
In the novels there seems to be something between Faramir and Aragorn. Faramir only wakes when he hears the voice of his 'King', and the at-first-glance adoration and loyalty is rather intense...
Not to mention the words between Aragorn and Éomer when they meet at the battle of the Pelennor Fields...
Then there's Aragorn and Boromir. The heartfelt, almost desperate confession in Lothlórien... And of course: My brother, my captain, my King. Boromir is the first person to acknowledge Aragorn as King, and basically propel him into wanting to be King at all.
The gender ratio being what it is, it's easy to see lots of Ho Yay in The Silmarillion as well. Ah, all the manly friendships out there...Maedhros/Fingon, Beleg/Túrin, Gil-galad/Elrond...Anything goes.