Brainiac 5 and Lyle Norg (aka Invisible Kid) had their share of Ho Yay. This mostly appears in the Post-Zero Hour incarnation of the team, where the two had a snarktastic rivalry over who was the better scientist. After Lyle had gone through a boom tube, Brainiac 5 is seen talking to himself about how Lyle relied on him, and when they find him the normally reserved Brainy hugs Lyle and kisses him on the cheek, while expressing his joy that he is all right.
In the very same run on those characters, Gear and Chuck Taine get a story to themselves involving them stealing some of Brainiac 5's inventions to make their job of clean up after the last adventure easier. Long story short, after destroying them, they end up bribing Brainy to be quiet about it with a letter telling him to be quiet about it or they'll tell everyone about his collection of photos including, amongst other female Legionnaires, Invisible Kid. Gives an entirely new meaning to the aforementioned kiss...
Salu Digby and Ayla Ranzz, especially during the Giffen-Bierbaum run, where it was pretty much explicit.
Since the return of Paul Levitz as Legion writer, Ayla and Salu are now an official couple even if they've never outright said "we're a couple," even though Ayla had originally been with Timber Wolf again when Geoff Johns brought the original Legion back.
Dude...Legion. Animated. Series. Brainiac 5 writes an honest to God slashfic with himself as a Purity Sue in the Relationship Sue-ish role, and has himself die gallantly in Superman's arms. Oh, I'm for real. In fact, Timber Wolf even lampshades this: . Then when he hears Superman is "back" he practically becomes giddy...then he sees it's not the "real" Superman (it's Supes' clone) and becomes quite pissy shall we say. This is after the Season One episode where Superman found a girlfriend, Lex Luthor's future offspring 'natch, and Brainy practically threw a hissy-fit and was about five seconds from drunk dialing Triplicate Girl to cry about it. Ho Yay doesn't even begin to describe it. It's outright fan service.
J. Torres: I definitely wanted to explore Brainy's "man crush" on Superman more. I also wanted to add Supergirl into the mix at one point and do some fun stuff with that "love triangle." I don't know if Brainy's love for Superman was of the romantic type, but then again, he has a 12th level intellect and his concept of platonic love versus romantic love is probably more complex than we could understand. I don't think we could accurately define it with our 21st century labels, nor would I necessarily want to in the context of this comic book.
Power Boy and newcomer Gravity Kid of the Legion Academy from Paul Levitz's run on Adventure Comics are officially a couple, and the two are currently working together with the Science Police on Takron-Galtos.