Rito and Mikan's relationship is all kinds of heartwarming, though you may have to overlook the Incest Subtext.
When Mikan gets sick, Rito spends takes over her chores and tries to cook her soup. Due to Lala's interference he messes up the cleaning and due to inexperience messes up the soup. Mikan chokes down the bad but not inedible soup and thanks him for the effort, calling him Onii-chan, which she very rarely calls him.
When Mikan feels lonely because Rito has been spending so much time with Lala, Rito immediately takes her out to try and cheer her up, which he eventually does.
When trying to stop Momo from sneaking into Rito's bed, Mikan tries to ambush her by hiding in Rito's bed while he's sleeping. Then thunder and lightning start, and Mikan gets scared. Rito, still asleep, immediately rolls over and hugs her, trying to comfort her. This is apparently something he's been doing since they were children whenever she got scared.
Rito calls Mikan a "special" existance to him, even more than a sibling, while describing their relationship to Yami.
Momo's relationship with Rito in Darkness. Despite the teasing she puts him through, it's clear she actually does care about the guy, and she puts far and away the most effort into taking care of him of all the haremettes. She's actually turned down his advances a few times because he was asleep or under the influence of something or other, because she wanted him to actually mean what he was doing.
Lala and Haruna trying to comfort Rito after he is forced to confess his current feelings about Lala in the Trouble Quest arc and things become akward. In the end, Haruna talks to him and allows him to admit that Lala is an important person to him without embarrassment, and Lala expresses her thanks that he's returned to normal and her regret that her younger sisters forced him to do something that he clearly didn't want to do.
Lala setting things up so that both Mikan's and Rito's parents can come home for Christmas. To put this into perspective, this is the first time they've all been together for potentially years.
Finding out that Lala intentionally let her inventions run loose in order to stop her younger sisters from fighting each other. She really can act like an older sister.
Yami refusing to battle Mikan when the latter was under mind control. She cared about Mikan too much.
Chapter 14 of Darkness: Yami tells Rito about her past, and even embraces him in her sleep. Also, her thought of "I want you to hold me."
Also, Yami's relationship with Tearju Lunatique, her creator.
Darkness, chapter 15 : Yami/Eve meets again with Tearju Lunatique.
Yami: What I'm thinking right now... is only one thing... "I am glad that you're alive." Just that... Tear...
The end of Yui's fantasy in Chapter 19 of Darkness definitely counts.
Chapter 21 - Rito comforting Nana about Mea breaking off their friendship. Also, Lala's conversation with Rito beforehand, when she basically tells him how much faith she has that he'll be able to cheer Nana up, simply because it's Rito.
Most of Nana and Rito's interactions that don't involve a lot of tsun are this. (Granted, there aren't many.)