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 154: "You truly prefer that boy over me? Even the love you gave me is his now?"
Special mention goes to an absolutely trope-smashing line from O'Brien in Episode 139: "Jim, was there . . . anything between you and Juudai?"
