Sho's jealous guarding of his status as little brother to Judai, his "aniki", in Yu-Gi-Oh! GX borders on Ho Yay (even more so in the dub). It turns into a really weird not-quite-love triangle when Johan appears in Season 3, making not only Sho but Judai's Stalker with a Crush so jealous, she possesses him.
No, you do not get away with merely linking to Dub Text. We're going to bring that quote over here: "Jaden's my best friend! He's my hero! He's the hot fudge on the sundae that is my life!"
Speaking of Yubel, its ever-ambiguous gender even extends to its past life as a human.
And let's not forget Saiou/Edo Phoenix, or the newly opened Fubuki/Yusuke Fujihara (from season 4)...
Edo and Ryo live together for part of season 3.
Ryo and Fubuki certainly seemed close before Fubuki disappeared...
A moderately-sized plot point for the third season is that Yubel (who is a hermaphrodite using male pronouns for "her"self; it should be noted that Juudai also refers to her as "he") believes that Juudai (who is male) loves/is infatuated with/spends too much time with Johan (also male). It's unclear if this is lampshading, or just YGO being YGO.
A special mention has to go to a piece of Ho Yay so blatant it borders on hilarious: while Yubel is utilizing Johan's body, she calls Juudai her beloved, tells him she will "show [him] the truth of [her] undying love," and even tells him "aishiteru, boku no Juudai" ("I love you, my Juudai"). Seeing screencaps with subtitles taken out of context may be enough to drive some Juudai/Johan fangirls straight into hysterics.
Episode 147 features "Johan" calling Juudai "my beloved" (or, depending on your subs, "in just a moment I'll show you the truth of my love"). While everyone around them gasps, Juudai just kind of stands there with no reaction whatsoever. One Japanese-to-Spanish fansubber takes the nuance even further: because of the different words for "love" in Spanish, the line translates from Japanese to Spanish to English as "In a few seconds I'll show you the truth of my desire, Juudai, my love." Given the context, there really is only one way to interpret that.
Here's a line from Yubel, talking to Juudai about Johan, in Episode 155: "Is your bond with him that important to you? Is that how much you prefer him? Even the love you gave me...It all belongs to him now, doesn't it?". It should be mentioned that Yubel used the word "suki" for "prefer" which also means love or like in a romantic way. So one could translate that line to "Is that how much you love him?" Note how Judai didn't react to what Yubel said to him but just continued the duel.
Special mention goes to an absolutely trope-smashing line from O'Brien in Episode 139: "Jim, was there . . . anything between you and Juudai?"
After Abidos the Third is defeated, he decides to return to the afterlife and asks Judai to come with him. He takes Judai's hand while he asks this, making it look like he's proposing. Judai blushes, but politely declines.