Natsume Yuujinchou: Natsume and Natori. In one episode of the anime, Natori asks Natsume to go to the hot springs with him, and shows up at his house with a bouquet of roses. It does not help that Natori is voiced by Akira Ishida, who voiced characters known for their Ho Yay like Kaworu Nagisa from Neon Genesis Evangelion, Fisheye from Sailor Moon and Xerxes Break from Pandora Hearts.
Same episode - Natori mentions to Natsume that if constantly lying to his foster family about the Youkai ever becomes too difficult, he can always come to him (please note, their futons are right next to each other at the time.)
Though taken another way (given that Natori had just been asking whether Natsume was happy with his foster parents), this has completely different connotations.
In the first episode of Zoku, Natsume commented on the Lord Youkai he had recently freed as being really cute.
And in terms of the Les Yay there's Hinoe's outright adoration and utter devotion to Reiko, her dislike of men (it's of great annoyance to her that Takashi Natsume looks so much like her Reiko yet is male), and her distraught reaction at hearing of Reiko's death, all which are anything but subtle.
Matoba/Natsume; though this could also enter Foe Yay territory. The second episode of the fourth season ramps it up by having Matoba invade Natsume's private space as he inches in on Natsume and practically whispers in his ear, in a "I have you now my pretty" manner. He also seems to enjoy grabbing Natsume by the wrist. And in the manga, he claims that he has written an "uncharacteristically long letter" to Natsume in attempt to persuade him to join the Matoba clan.
Tanuma/Natsume; In a humorous scene ( Season 3, Episode 10 ), both awkwardly blush and smile at each other as the background turns a shoujo manga pink.
