In the manga, Ruri sees Takuto and Sugata together and incorrectly assumes they're a "pretty boy couple."
Takuto also spends every weekend at Sugata's house "so he won't be lonely." Before his dorm room burns up in the midst of out-of-control fireworks and he has to start living with him.
Takuto and Sugata are seen having baths together three times.
Head telling Sugata he's happy that "someone as beautiful as him lives on the island"...
With Sugata coming back to "watch him paint"...
Episode 14 takes this Up to Eleven: Head tells Sugata that painting what he loves is his idea of happiness. Next, he suggests painting a portrait of Sugata.
Episode 23 isn't even subtle about it: Sugata receives the painting Head made of him... and Taiga and Jaguar quickly comment that it has an unpleasant libido on it. Yeah...
Kanako and Simone have bittersweet vibes going after Simone's back story comes up in the series.
Madoka and Kou are basically confirmed as canon.
And then it turns out that Kanako and Madoka had a relationship together in the past. And Simone seems rather jealous to know that.
Head and Shingo are basically canon, and don't seem shy about expressing it in public.
Head and Ryousuke also. Ryousuke's the only person still around on the island who cares for Head's well-being, and missesthe Tokio who once picked up a paint brush without being totally consumed by a want for power from the Cybodies. Their dynamic seems similar to that of Sugata and Takuto's, and seems to be no coincidence that the one to inspire Head to paint again mirrors in temperament and circumstance.
Kanako and Simone have so many bittersweet vibes going on between them (though one could consider them squicky, due to Simone being Watanabe's step daughter, servant and classmate. All at once.