See FoeYay for this show's large cache of thoroughly creepy subtext.
For some straight (ha ha) Ho Yay or rather Les Yay among the heroes, you'll notice Raven and Starfire get awfully attached to each other as the series goes on. Check out the episode "Fear Itself" where the Titans get captured one by one by some kind of nightmare creature taking over their base. Starfire's capture is the only one where Raven shows visible concern and worry. She didn't even bat an eye at Beast Boy's capture and he's the one she's frequently shipped with!
Starfire is thrown into a temporal vortex in the episode "How Long Is Forever?". She lands in a world where she's been lost for several years, and it turns out that the Titans were so dispirited and sad after her disappearance, that they have been disbanded and haven't seen each other for years. After her disappearance Raven went the Maddened Into Misanthropy way.
Starfire and Raven also do the Security Cling in one episode to each other when Beast Boy scares them and Starfire has a tendency to glomp all her friends, especially Terra and Raven. Starfire is also quite affectionate towards Raven.
Fans believes either that the fight between Raven and Terra in "Aftershock part 1" was for Beast Boy's love, or that Raven acts as a Woman Scorned due to her snapping when Terra mocked her about "actually believing I was your friend". Nevermind Raven was shown to have animosity toward Terra since the beginning, meaning this might have caused all her anger against her to pop up.
In the Bad Future episode, where due to Starfire's disappearance Raven went insane. As opposed to Starfire's canon love interest, Robin, who apparently moved on pretty well (then again, Robin was trained by The GoddamnedBatman).
Robin and Cyborg also have a fair bit of Ho Yay, with one early episode featuring them having a fight and "breaking up" for awhile, with the whole thing played a lot like a boyfriend/girlfriend spat. There's also numerous scenes of them working out together in the gym, despite being completely different physical types with wholly different training requirements.
And Cyborg and Beast Boy are at the very least Those Two Guys, which pretty much automatically confers Ho Yay for some. Beast Boy's absolute, utter delight at having a Cyborg replica of his very own to play with has no doubt caused many a Rule 34 bit of imagining.