Yukari and Reimu's relationship as mother and, be it adopted, daughter.
For two girls that were once enemies, Kaguya and Mokou sure do get along just fine and even think of each other as sisters.
Ran and Ren's relationship is rather sweet.
Yukari being reunited with Reimu at the end of Gensokyo 20XX
Chen comforting Yukari in 20XXI
What Reimu said during her narration of Chapter 7:
It didn't matter if she had brought me with her or left me behind because neither one could guarantee my survival. Nevertheless, I do not hold it against her, as she did what she's had to do. If I were to freeze to death tonight, I would never hold it against her.
In 20XXI, we're treated to how Suika feels about Reimu.
I wish Reimu were here with me, then I wouldn't be alone. Reimu is my best friend and is more than willing to keep me company, even if she is age-regressed. Toddlers are funny, aren't they? She likes me a whole lot and likes to climb on me but she isn't here to do that. They had better not hurt Reimu. They can beat the hell out of me but they will sure as holy hell not lay a finger on Reimu. If there is so much as one hair missing from Reimu's head, heads are going to roll and I am bringing all my peoples!
In 20XXII, what Satori said to Ran.:
"We're all thinking the same thing you are thinking, you can cry now. You're stronger if you cry."
And her comforting Nitori in chapter 12 after the latter attempted suicide.
When Kaguya asks Mokou, "Can we be sisters now?" and Mokou's response that she likes the idea, even though she'll slug at her when she gets mad at her and every other Tuesday.
In Chapter 27 of Gensokyo 20XXII, we have Mokou comforting Ran and asking Keine to look after Ran's now deceased pup.
Also, from the same chapter, we have Keine and Yume's (Ran's pup) walking down the hall holding hands
In 43 of 20XXII, Kaguya's reason for not escaping.
"You know I really couldn't do that, after all the rest of you are here and I don't want to be alone. I can't stand freedom if it means being alone and leaving behind my sister. I'll stay here."
In the same chapter, we find out Suika's reason for escaping.
To a subtle degree towards the end, Yukari whispering, "My beautiful babies". It is rather sweet that not only did she acknowledge Ran as her perceptive offspring as well as she did Reimu, she showed that Ran is always beautiful to her, no matter how scarred up she was.
Life in Gensokyo Village
Chapter II of Life in Gensokyo Village has Kaguya cheering up Mokou, when the latter feels sad about Keine's death, remembering that she used to cook new dishes, and the two making and having dinner together.
In Chapter six, we have what Suika says to Yukari, when the latter doubts she will find love.
"Aw, shucks, even if you are soiled, barren, and is old, someone will still find you to be the prettiest in the whole wide world. I mean, look at Ran, she's scarred up and has endured hardship but there is a kitsune that loves her and finds her to be seductive. Them other kitsune are shallow but, not this one, and he is adorable. You're beautiful, fat ass, and someone will think so, too."
Reimu cuddling Tewi and Tewi cuddling back
Suika comforting and reassuring Reimu and Chen that Yukari will come back in chapter 24
Yukari taking in Maribel and Renko
In chapter 3, Mokou taking Kaguya's ragged mittens and giving her her own mittens is rather sweet.
Chapter 7 Laaa! is rather sweet and adorable.
Suika comforting Chen in chapter 10.
Yuuka waking up during and comforting Chen after her nightmares in Chapter 18
And she comforts Chen again in chapter 29.
The other comforting Miko when she tells them she is going blind
Satori comforting Yukari out of suicide.
The ending of Chapter 62 Chen's Suicide Note: Reconciliation.
The Next Chapter, where is it narrated by Flandre, who notes that Chen is still Chen, which is sweet in that she can see past her disabilities.
Flandre: Either way, she is still Chen and Chen is Chen, even if she can't talk.
Chen inviting Miko over for dinner and the resulting events is rather sweet.
Ren telling his wife she should get some sleep and that he'll take over.
Reimu comforting Satori in chapter 17.
Reimu befriending a resurrected Reisin in chapter 23.
Kaguya: Naturally, the two made friends by hitting, only Reimu threw the first hit and Reisin responded. Reisin was kind of a wild sort but a gaze into her eyes made her calm down and flop onto her stomach, resolving whatever conflict was there. The two spent about an hour looking at each other, their eyes never looking away from one another's. After looking at each other, being locked in some sort of stare-down, they went about their own business before engaging in playful behavior, Reisin, it seems found an equal.
In the next chapter, we have Ran demanding that her blood be placed into Reimu, so her life could be saved. While she is arguing with Kaguya on the ramifications of it, Chen comes forward saying, "Take my bwood, then, if Wan-mommie's won't wowk." and the others following suit.
Chapter 30, we have Reimu singing a little song about her enjoying life despite being pretty close to blind. According to the author's note, she is singing that to whoever will listen, which is rather sweet in itself.
Chapter 38, we are treated very well to a bit more how Ren feels about Reimu and Chen, especially, when he stands up for the latter when his brother called her a little monster and comforting her of it afterwards.
Ren: No, no, sweetheart, you're not a monster, Baka's just being a whinyass.
From chapter 55, we have this from Chen:
Frankly, I wouldn't trade these motherfuckers away for any other ones. Sure, some of the time I can't fucking stand them but, at the same, I love these motherfuckers and can't live without 'em.