These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Ho Yay: In the manga at least, Nokoru and Suoh. Suoh knows every detail of Nokoru's life over the previous three years. Both boys are seen as loners to those who know them well, and the people around them initially express surprise when they take interest in one another. Physically, they could almost be seen as the template for many other CLAMP pairings - The tall dark (or blue...) haired guy with the shorter blond guy - sound familiar? Retroactively, the two draw some very close comparisons to Tsubasa's Fay and Kurogane, right down to the scene where Suoh holds Nokoru after he's been shot. It closely mirrors the aftermath of the Eye Scream incident in the Acid Tokyo arc. There's also a Say My Name moment, although not much attention is paid to it. Add to that the massive emphasis put on telling the story of how Nokoru and Suoh became friends, compared to the nods they give to Suoh's relationship with Nagisa. And of course, there's all that stuff about Suoh and the person who will determine his destiny. Suoh is very protective of Nokoru and talks about "staying by Nokoru's side" and "choosing to follow him" in a manner that suggests Nokoru is more to him than just a friend.)
Toy Ship: Kinda inevitable when you three cute and chivalrous grade-school kids out to help older women, and when you have two with canon love interests.