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 itís just friends is it? How disappointing.
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.
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.
A couple of Little Busters! examples: 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.
Very, very darkly used in School Days. In one of Kotonoha's routes, a bunch of girls (Nanami, Hikari, Otome and Otome's Girl Posse) decide that Makoto is better off with the aforementioned girl's love rival Sekai (also a friend of them). What will they do to make sure Makoto will "choose the right girl"? Treat the "girl in between"like utter shit! Nanami and Hikari verbally threaten Koto at first, then help Otome and Co.'s already present bullying via spreading rumors aboutKoto beind a slutty "phromone girl", and then they tip off the Girl Posse so they can destroy a lunch that Kotonoha made with lots of effort for him. The results will be very different, depending on whether Makoto finds out or not, and none of them will be kind to Sekai: on one hand, if he finds out about this drama he'll go Tranquil Fury on the girls and cut all ties with Sekai, then commit himself solely to Kotonoha; and on the other, if he does NOT find out, Kotonoha will massivelysnapon Sekaiand give her a fatal case of Slashed Throat, in broad daylight and in front of Makoto.
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 Phoenix Wright: Ace Attorney, 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.
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.