a2 ~a due~: In all the routes with good endings, it seems that the entire orchestra wants Hao and Sona to hook up. Somewhat understandable, as the two are very close by this point and are always spending time together.
French horn player: It's because you love us, don't you, Sona?
Cello player: But not as much as you love Hao~.
Sona: You're getting your face punched in first, just so you know.
Riko in A Profile is pretty forward about her desire to see her daughter hook up with her step son. Masayuki is slightly unnerved about the matter.
Mikiya and Mischa to Yukiha and Eri in the latter's route. The two even set them up on a lunch date, and Mischa forces Yukiha to feed Eri, much to both parties' chagrin. When Eri complains that she couldn't even taste anything because she was feeling so embarrassed, Mischa quickly tells Yukiha to give her another taste.
In the second game, Rina and Kazuha in the Yukitsuki route. Rina notably makes a lot of teasing comments but is generally supportive of the ship. As for Kazuha, she even gets Yukitsuki to feed Kyoichi after convincing her that he can't move; unlike Eri, Kyoichi is Genre Savvy enough to realize that if he told them he couldn't taste anything, Kazuha would just make Yukitsuki feed him again.
If you (as Hisao) pick either Hanako or Lilly's route, the girl who's not chosen will support you trying to gain the other one's affections, each in their own ways. It may be a Matchmaker Crush in the case of Hanako, though it's not openly stated.
Also, in Hanako's route, Miki will talk to Hisao at some point and wonder if he and Hanako are a couple or not. The reply you give her will make you either gain or lose points with Hanako, thus pushing you either to the Good, Bad or Neutral Endings.
Rin also sorta supports Emi and Hisao in their route. At some point Emi and Hisao almost break up and they have a fight in the presence of Rin. She gets fed up and leaves the rooftop so they can discuss their matters and fix them up.
Akira supports Hisao's relationship with her younger sister Lilly, in Lilly's route.
The biggest example is Misha, who shows shades of this in several routes:
In the case of Hanako, she'll bring Shizune along. They'll ship it both because of cuteness (in Misha's case) and because they do care for Hanako, despite Shizune's difficulties with Lilly (because she's Hanako's Only Friend at first, they can't get to Hanako without seeing Lilly) and their huge workload.
She will also voice her Hisao/Shizune shipping if you go through her best friend Shizune's route. Then it's subverted when you find out that this is more of a Matchmaker Crush... because Misha is in love with Shizune.
She also grins widely after finding out that Hisao and Lilly are a couple, having refused to believe Hisao's claims that nothing out of the ordinary happened on their trip to Hokkaido.
Finally, Misha also shows support of Hisao's relationship with Emi, should the player pursue her route. ("Young love is so unpredictable, isn't it~!"). And even more so: if you choose the wrong option and Hisao gets thrown outta Emi's house as a result, Misha will come to the rescue and openly force him face what he did. Like in Miki's case, getting either the Bad or the Good Ending depends on what you (as Hisao) reply to her. (This may include Shizune too, as it turns out that Shizune was the one who told her to go help Hisao in the first place.)
Lilly also ships Hisao/Emi on her only post-Act 1 appearance in Emi's route.
Lilly: (teasingly) Ah, so it’s just friends is it? How disappointing.
Mio, as a Yaoi Fangirl, naturally ships Riki/Kyousuke, sighing with a smile when she hears how they used to hold hands when they were younger and telling him to treasure their friendship forever.
Kyousuke, on the other hand, in an aversion of My Sister Is Off-Limits!, ships Riki/Rin, as he thinks that if the two of them are together they can achieve much more than if they're on their own.
Masato and Kengo also come across like they ship Riki/Kyousuke at times - many of Kengo's Embarrassing Nicknames used in the fighting minigame tease them about their feelings for each other (e.g., both can get 'Honorary Member of the ____ Love Club', referring to one another), and while Masato is initially surprised when he hears that Rik might like Kyousuke, when Riki denies it, Masato says that's a shame as they'd make a good couple.
Morenatsu has Amaki Tsukishiro, who actively ships Hiroyuki and Shin if you play Shin's route. Shin and Hiroyuki both deny everything, and Shin even tends to get mad at Amaki for doing it.
Pearl Fey ships Phoenix/Maya like mad. To the point where she'll slap poor Phoenix unconscious if it looks like he's being unfaithful to his "sweetheart". It's not that simple, however: Pearl ships Phoenix/Maya THAT hard because she has never seen a sucessful romance in all her short life, and in her child-like mindset she wants to make sure Maya will be happy.
To lesser extent Maya herself ships Phoenix/Iris practically from the moment these two have met in Hazakura, playfully teasing him about his supposed falling in love for her.
In Spirit of Justice, Dhurke tells Apollo that Trucy would make a good wife. In front of her. They're actually half-siblings, but neither he nor they know it.
In Queen's Gambit, Cassidy, the little sister of the protagonist, has this reaction towards two potential love interests and the main character, "Shield." In the case of Emmett, he has been Shield's co-worker for nearly eight years. João on the other hand, is new to the scene but the fact that he shows up to visit Shield in Vegas while his home is in Brazil tips Cassidy off big time.
In a less dark manner, Sekai's mother Youko supports her daughter's affection for Makoto. Unless you make Makoto pursue her in the spin offs. Similarly, Kotonoha's mother Manami and little sister Kokoro ship Kotonoha/Makoto. Again, unless you make Makoto pursue them in the spin offs.
In Sickness, Karasu will not stop bringing up wanting Suoh and Misa to hook up, much to the dismay of her father.
Flashbacks in Sunrider Mask of Arcadius show that Kayto’s younger sister Maray shipped him with his childhood friend Ava. When she saw the two of them sneaking into Ava’s apartment to have their first time, she was thrilled and covered for Kayto when their mother asked if he was home yet.
During the Beach Episode of the same game, Icari and Claude go out of their way to get the shy Chigara to admit her feelings for Kayto, even going so far as to get Ava blind stinking drunk so she can’t interfere. This is rather odd on Claude’s part, considering her own blatant lust for Kayto. The end of Sunrider Liberation Day puts a sinister spin on this: Chigara is a Prototypespysent to seduce Kayto, and Claude—who is working with the Prototypes—is pushing the two of them together to ensure that it happens.
Sunrider Academy's swim team ship their captain with Kayto, going so far as to hold up these signs at the national championships:
Shion Sonozaki, Mion's twin sister, supports both her sister's affections for Keiichi, and Keiichi's affections for Rena.
Satoko seems to be just fine with Shion's affections for Satoshi, though it's debatable whether she really notices it.
Nurse Takano and Tomitake seem to ship Keiichi and Rena too.
In Umineko: When They Cry, Shannon ships Kanon/Jessica. In return, Jessica ships Shannon/George. Considering that later games heavily imply that Kanon and Shannon are the same person (which the manga confirms), it makes the earlier shipping scenes rather awkward in context.
In Danganronpa, Junko-as-Monokuma asks Naegi if he and Kyoko have been screwing, and eagerly describes the erotic acts it thinks they might have done. In an earlier chapter, Aoi spontaneously advises Makoto on how to impress Kyoko.
Ano from Kindred Spirits on the Roof is a Yuri Fan who likes to imagine yuri couples among the other students at school, but she fully admits that it's just for fun and has no interest in any actual romance. Nena also subtly tries to encourage Sasa to confess her feelings for Umi after she realises what's happening.
In Yuzuki's route, his big brother mentors Aoi and Souji ship him with the Player Character too. Again, they do it before the Gender Reveal, and they explicitely say that they don't see anything wrong with two guys in love. Then again, if Yuzuki is romanced he falls for the PC before the reveal as well and later pretty much states that he's bi after that...