Chapter 21 of Broken Saints features a tender moment between Shandala and Oran that can be interpreted this way, although it also has a platonic skew as well, since...well, since she's All-Loving Hero - she can be tender with whoever she wants.
Also, in the Chick's "11 Embarrassing Nostalgic Dance Crazes", the Chick mentions a date that Nella set her up on. Flashback to the Chick and the Critic on an awkward date.
In his Kickassia commentary, Doug says that calling her "Mrs. Vice-President" was a mistake but he couldn't be bothered to edit it out. So yay happy accidents!
Not so much anymore, but there was always a little bit of this with Critic's crossovers with the Nerd, especially with the term "Nerd-on-Critic action" being thrown around. Best described on their Foe Yay section.
And then there's Critic/Lupa in Suburban Knights. Even lampshaded by the commentaries as playing to the fem!dom lovers in the fandom.
It also takes a moment to tease Lupa with Angry Joe, who finds Lupa in Snow White cosplay sporting a leather jacket and wielding a semiautomatic to be extremely hot.
Draco and Hermione get a lot during A Very Potter Musical. He has a crush on her but she hooks up with Ron. Then A Very Potter Sequel, which is set one year later, has a ton for Hermione and Ron, showing how they ended up hooking up.
Despite Dorian's roleplayer saying that she wouldn't ship him with anyone and Susan Xian's roleplayer's major disinterest in Shipping at all (yes; Wilson's roleplayer is also Susan's), the two characters have a few moments that could be interpreted as this.
Madigan Hightop and Bernard "Bernie" Stewart have a little of this since the latter seems to like her the most out of everyone else. Though neither roleplayer had thought about shipping them with anyone at first since Madigan is twelve and Bernie is fourteen.
Mathew and Fawn seem to have developed a few possible feelings for each other despite not knowing each other for too long.
Cass Hackwrench and Augustin also seem to get along fairly well, despite the slight Furry Confusion.
There is some between Ted and Delta, though until recently it seemed to be awfully one-sided on poor Ted's part. (It still is, but now there's been a slight hint that she might like him as well.)
The War Comms has this all over the place. Zacharias/Esmeralda, Kristan/Morgan, Alyssia/Hannah, Missy/Trisha, Missy/Esmeralda, Syrius has it with three different people (Molly, Julia and Ralph), Janet/Alyssia...
Due to Noob having a couple of more or less official couples (one of which only lasted about a season) for a little more than twenty characters, many pairs that seem a little closer to each other than to the rest of their circle come off as this. Also, the fact that one of the characters is a Yaoi Fangirl who keeps picturing two of the male characters together makes same-sex shipping feel less of a leap than in most series.
Nora is attracted to Ren, and the two have a very close friendship.
Nora: We've been friends for soooooooo long! What are the odds we'd still be together? Well, not "together-together"... Not that I'm not saying that you're not handsome; you are handsome, but that'd just be weird, right?
Pyrrha saves Jaune's life despite barely knowing him, and later becomes his mentor, unlocking his magical ability with a spoken vow that sounds vaguely romantic. Technically, this shows her compassionate nature, but you can see why people ship them. Also not helping matters is the fact that she actively seeks him out during the initiation to be his partner, despite having only spoken to him once before.
They also have an instrumental theme that only plays when they're together. For the developers to put such effort into establishing a mere 'friendship' is...suspicious.
The episode "Extracurricular" confirms this: Pyrrha likes Jaune, and is visibly hurt when he goes after Weiss. For his part, although he considers Pyrrha attractive, Jaune doesn't see her that way.
"Dance, Dance, Infiltration" is just dripping with shipping. Jaune finds out Neptune turned Weiss down, but before he can chew him out, he sees Pyrrha off by herself. She confides in him that he's the only person to ever treat her like an equal and that he's the kind of guy she'd like. Moments later, Neptune walks up, and he and Jaune have a heart-to-heart. We find out that Neptune turned Weiss down because he can't dance and is quite embarrassed by that. Jaune gives Neptune the same advice Pyrrha gave him, "Just Be Yourself." As Neptune goes off to talk to Weiss, Juane says he has only one thing left to do. Moments later, we see Jaune walk back into the dance wearing a dress (like he said he would if she arrived without a date) and offering to dance with Pyrrha, which she gladly accepts.
Also, Blake and Sun can be seen dancing together, Ren and Nora apparently came to the dance together, and Ironwood manages to get a dance from Goodwitch.
Ozpin and Glynda are nearly always seen together and constantly act like the students' 'parents'. In Episode 1, the glance between them resembles that of an old married couple. When the staff was asked by fans what their relationship really is, the staff joked that they "share a toothbrush" and avoided answering the question. Although Glynda appears constantly disgusted by Ironwood's persistent interest in her, she ends up politely dancing with him at the ball - but only after she first glances at Ozpin and he silently nods his permission to her.
In volume 2, Neptune successfully flirted with Weiss note much to the shock of the fandom, who had assumed she was gay. Later, she tried to partner with him when their teams went on a mission.