Ah... and Mm... Are All She Says: Tanaka holds Toda's hand when they're on a rollercoaster both are afraid of, breaking Toda out of her flashback.
Berserk: Guts and Casca joke about holding hands and actually do hold hands once their relationship is affirmed.
Beyond the Boundary: Happens a lot with Akihito and Mirai. In fact, their interactions as a couple generally consist of either holding hands... or Mirai crying into Akihito's chest. Surprisingly it still works given their backstories and how their relationship evolves. And by the time the finale movie rolls around, holding hands is more significant and symbolic for these two that they opt to do this rather than kiss during the moment they finally get together.
Bitter Virgin: The very last image has Daisuke and Hinako doing this, immediately after both had silently admitted to themselves that they didn't expect their relationship to last and wanted the other to find someone who'd be a "better fit" for them. The scene enhances the final question of whether their relationship really is doomed as everyone thinks or not.
Bleach: In a cover page, Rukia and Orihime are shown doing this. NAKED.
D.Gray-Man: A Tear Jerker example happens when For arranges Bak's deceased parents after they were killed by Alma so that they were leaning against each other and holding hands.
The Dangers in My Heart: On their first out-of-school hangout, Anna has Kyōtarō hold one side of a shopping bag with her, apparently to keep them from getting separated. There also happens to be a couple holding hands behind them. Eventually they’re forced into holding hands for real when a crowd of people nearly separate them on a train. They kept holding hands on their way home, unsure of when to let go and walking very slowly.
Eureka Seven: Renton and Eureka do this a lot. It starts when Renton saves Eureka from falling while they were in the sea of rainbow clouds after he leaves Ray and Charles and Eureka starts looking for him, though that may count as a Take My Hand! moment as well.
Fly Me to the Moon: The two leads start their marriage with "all-you-can-grab" handholding.
Fruits Basket: About a third of the way through, on the way back from an errand, Kagura wants Kyo to hold hands with her. After causing a scene when refusing, he agrees just to get her to be quiet.
Fullmetal Alchemist: Subverted in the anime. Mustang and Hawkeye are standing side by side at Hughes's grave, and the camera is placed behind them suggestively, but the hand-hold never happens.
Haruhi Suzumiya: At the end of The Disappearance of Haruhi Suzumiya, Kyon holds Nagato's hand when promising to defend her against the Data Integration Thought Entity.
Arslan frequently greets his companions like this, such as when they were all reunited after being separated on the journey to Peshwar and again after he was exiled by his father, indicating that he sees them as friends rather than servants.
One instance has Daryun doing this to Arslan to reassure the young prince that regardless who he is, he is Daryun's beloved lord. It's particularly notable because Daryun removed his gloves when he does this to convey his sincerity more.
His and Her Circumstances. When the girl didn't know how to show her love for the boy, she held his hand during the student council meeting.
I Think Our Son Is Gay: Chapter 16 is about this. Hiroki notices some of his classmates doing this as he's shopping with Tomoko. Tomoko asks if he would do that with his crush, and Hiroki, who is gay and closeted, sounds extremely relucant, only considering that if it can be done when in private. Tomoko tells Hiroki that the latter was how she and Akiyoshi did when they were dating since he was easily embarassed, and makes a mental note of making him more comfortable with his sexuality.
Junjou Romantica: The couples are shown holding hands along with Intertwined Fingers in the opening sequence. It's rarer in the manga or anime, highlighting the seeming reluctance of some of the characters to pair up.
Kaiju Girl Caramelise: This is the central event of an important scene in the first chapter. Kuroe Akaishi is a high school girl who undergoes Involuntary Shapeshifting of parts of her body as a result of strong emotions, so she becomes an antisocial loner to avoid any incidents. When her popular and handsome classmate Arata Minami ropes her into going on a kinda-sorta date with him, a Girl Posse from their school catches sight of them walking together and audibly protest such an "ugly chick" being with the school heartthrob. Arata defiantly holds Kuroe's hand in response; Kuroe is so overwhelmed by this gesture that her emotions get the better of her and she fully transforms into a Kaiju for the first time.
Katanagatari: Togame and Shichika finally do this in Episode 11 against the sunset to the Squee of many. It makes what happens right afterwards more heartwrenching.
In the first instance, Rikuo has to hold Kazahaya's hand while they watch a movie together, because Kazahaya is too sick to get the information they need from it unless he channels Rikuo's vision. Kazahaya isn't exactly thrilled about all the Ho Yay implications.
Later, the two have to search for a vase in a pitch-dark shrine. When they discover that it's Bigger on the Inside, they decide to hold hands to keep from getting separated. It isn't until they realize that not only does the other apparently smell like flowers, but that the hand they're holding is too small to belong to a teenage boy, that they discover that the spirit of the vase has been leading them around in the darkness all this time, just for giggles.
In the climax, this is one of the first steps taken by Nanoha and Fate to show their then budding relationship, with Nanoha holding Fate by her hand and Fate responding by grasping Nanoha's between both of hers. It's also worth pointing out that Fate normally has an aversion to physical contact due to her experience with Precia, making this an extreme act of trust on her part.
Lindy holds Fate's hand in A's to comfort her after she wakes up following being ambushed. While it does make her blush, she clearly enjoyed the display of parental affection.
Erio and Caro hold hands while air-dropping into their first battle during StrikerS.
The second movie has several scenes that focused on Nanoha and Fate holding hands that reflected Fate's confidence as a person. At first, Fate was only able to offer her hand to Nanoha, but in the end she's able to reach out and take Nanoha's hand on her own.
Nabari no Ou: Miharu and Yoite do this when running away from Kairoushuu. Yoite later thanks Miharu for "never letting go" of his hand right before he dies.
This happens between Naruto and Hinata, after the latter delivers a Get A Hold Of Yourself Man to the former in Chapter 615. Given their general reactions, it's definitely presented in a romantic way. This frequently gets a Call-Back throughout the rest of the franchise and especially in some of Shippuden's later openings and endings. It even made its way to one of the manga's volume covers (specifically, volume 64) and some merchandise. This is actually a large part of Hinata's character arc: the one thing she always wanted was to catch up to Naruto and hold his hand.
Naruto and Hinata hold hands again several times in the climax of the Canon movie The Last: Naruto the Movie, as one of the final preludes to the two of them finally becoming a couple.
Shikamaru/Temari and Sai/Ino are seen holding hands in the final episode, signifying that they have officially started dating.
No. 6: Shion and Nezumi hold hands while sitting on the same bed, no less.
Ojojojo: Haru and Tsurezure hold hands for the first time in Chapter 20. It should be noted that they had already been a couple for several weeks at that point.
Robin meets her mother for the first time and was just so happy to hold her mother's hand despite the entire island of Ohara going up in flames.
Robin: I've wanted to do this for a long time.
In a flashback on Fisher Tiger, a human girl Koala went up to him and held his hand, despite his attempts to swat her hand away. What makes it particularly outstanding is that Fisher Tiger was enslaved by humans and here, he allows a human to hold his hand. Not to mention how humans have cruelly discriminated fishmen and how fishmen bitterly hated humans in return, this little act spoke volumes.
Pokémon: The Series: Happens from time to time platonically, but a significant one is in XYZ, where Serena's weakened Eevee holds her hand...not with her paw, but with a Sylveon feeler, signifying her evolution.
Pokémon Adventures: In the RS arc, Winona allows herself and Wallace to briefly hold hands before they go off for battle, hinting that she might be interested in rekindling their past (failed) relationship.
Pretty Cure: Crops up frequently, especially between Cures that have dual transformations, and even more so between the original duo, Nagisa and Honoka, who power up their finisher by squeezing each other's hands harder.
In a story epilogue, Ranma and Akane are walking home together after a dangerous (and relationship-defining) adventure in the forest of Ryugenzawa. Desperately trying to convey his affection for her, but completely at a loss as to how, he reaches back awkwardly and hesitantly. Akane notices, and takes his hand — in the animated version, this disarms him completely, whereas in the manga this makes him even more nervous than ever before.
Ranma: Today, I can't seem to meet your gaze. Akane: In my whole life, I've not felt this way before. Ranma and Akane: Can't say it aloud. Let's just keep it quiet for now. Ranma: Without words, your hand in mine's enough.
In one episode, Genma goes home to the Tendo household, after being lost for several days, and sees Ranma and Akane arguing. He cuts out the middleman (Who needs romantic buildup, anyway?) and puts their hands together himself. It actually shuts them up for once and they look at him with surprise while he quietly sips his tea.
After Ranma and Akane eat love mushrooms, Ryoga, Mousse, and Kuno chase after them. When they find the two of them walking up the mountain, holding hands, they know things have gotten serious.
Roll Over and Die: Happens frequently between Flum and Milkit. It gets to the point they’ll always be holding each other’s hand when they walk next to each other whether it is on a shopping date or entering hostile territory. The first promotional artwork of the manga has Flum and Milkit holding hands as Flum prepares to face against an Spiral Ogre monster.
In Act 1, Usagi's second recurring dream of a romance between a prince and princess, her view of the dream princess changes to a first-person perspective, in which she sees herself running while holding tight to the sword-wielding prince.
The Closing Credits, which detail a romantic rendezvous, open with a close-up on Serenity and Endymion's clasped hands as they walk to the ocean shoreline, while the Ending Theme's first lyric is "Let's hold hands".
Simoun: The group variation is done towards the end, where the survivors of Chor Tempest hold hands as they walk together into the Spring for their final gender assignment. This is in particular contrast to the original Chor Tempest members' visit to the Spring at the beginning of the series: they go in separately and alone, and the whole ordeal is a lot more traumatic for each of them.
Spirited Away: Haku and Chihiro first hold hands after Chihiro helps Haku remember his name. Also justified since they were free falling from the sky and Haku can fly. After this they continue to hold hands whenever they're in touching distance of each other.
Shizuku and Kaori, who are playing at being in a relationship but do have actual feelings for each other, do this in Chapter 13, on the way to meeting Ruri and Seri.
In the final chapter, Shizuku and Kaori are shown this way in the panel in which Kaori, in her posthumous letter, expresses her wish that they could have been an actual couple, with the holding hands part being shorthand for being a couple.
Summer Wars: Kenji holds Natsuki's hand to comfort her after her great-grandmother's death, complete with Intertwined Fingers.
Sword Art Online: When trapped inside the nest of an ice dragon, Lisbeth ask Kirito to hold her hand before falling asleep. She then comments how warm it is, even though they're nothing but data inside a virtual world. After their adventure, Lisbeth confides to Kirito that she has been looking for something real in that world, and she found it in the warmth of his hands.
Tamagotchi! Yume Kira Dream: In episode 3, Himespetchi sees Mametchi holding Yumemitchi when she almost trips, notices they're holding hands, mistakenly assumes they're doing so because they're in love with each other, and faints from seeing it. After she wakes up from fainting, she realizes the two weren't holding hands because they love each other and sighs in relief.
Washio Sumi Is a Hero: Washio and Sonoko hold hands while watching fireworks during a summer festival.
Yu-Gi-Oh!: DefiedFor Laughs when a magic ritual requires the gang to form a circle and hold hands. Joey and Tristan don't look too comfortable with this and end up just touching fingertips.
