Berserk: Casca upon seeing Guts alive after the 100 men slaughter.
In Sasami: Magical Girls Club, after a confession gone wrong, Monta assures Misao (awkwardly) that her magical powers aren't creepy and don't make him hate her, and she starts to tear up. That's when Sasami shows up, and seeing the tears, asks if Monta made her cry. Misao quickly tells her friend that these are tears of joy.
Very funny example in Baccano! when Jacuzzi shows Nice his new face tattoo. He thinks she's crying out of sadness and he starts crying too because he hates making her upset, but she's actually happy.
And she does when Ed and Al return home in the final chapter and Al has his body back.
Also Lan Fan, when she receives a message from Ling saying that he's found a secret to immortality, which will ensure their clan's survival. But when her initial joy passes, she suspects that there's more, and Al is forced to admit that Ling is the new Greed.
Rozen Maiden: Traumend — Shinku revisited by Suigintou, and it's not an empty dream this time.
In Chapter 450 of Naruto, Iruka seems to be shedding a single tear after seeing Naruto being welcomed back to the village after defeating Pein, after having a flashback in which he remembers how much of an outcast Naruto was before. Considering that Iruka is essentially Naruto's father figure, this is both appropriate, awesome, and heartwarming.
From the same chapter, Hinata, after Naruto comes back alive.
This happens again when Minato starts crying the moment his son, Naruto, is born.
Chapter 488: Shizune crying when Tsunade wakes up from her coma, and then hugging her.
Nanoha in the penultimate episode of Magical Girl Lyrical Nanoha StrikerS, when after certain events that had a few instances of You're Not My Mother being invoked, she is finally reunited with her adopted daughter. Although the tears didn't start flowing until she saw her daughter standing back up on her own two feet just like Nanoha tried to teach her before, saying that she had promised her Nanoha-mama that she'd be strong.
Also Brook cried after Luffy told him that his friend Laboon was still alive and still waiting for him.
Jinbei shed Manly Tears when Nami told him that she forgave him.
Koala broke down into these when Fisher Tiger changed her slave mark into a sun mark, told her it is OK to cry (Breaking her Stepford Smiler façade in the process), and vowed to return her home.
Luffy can only burst into tears when in chapter 731, Sabo reveals that he is alive.
Vash does this occasionally, though never in serious scenes; he doesn't get that happy. Relief that everybody survived a particular snafu gives him the fountain-eyes, though.
Meanwhile, in a far more horrible example, poor Legato Bluesummers in his flashback story to his childhood—his telepathic powers allowed him to instinctively survive when Knives sliced apart the building in which he was being raped to death and all other occupants. He then kneels in front of Knives, who is his new instant god, and says he'll release his power and let Knives kill him in a moment with the angel-arm blade at his throat, but...he would like to stay by his side.
In Mai-Otome, Akane's two room attendants, Erstin and Irina, have this after she decides to elope with Kazuya instead of becoming Florence's Otome.
Bakuman。 lampshades this in Chapter 99, "Tears of Joy and Tears of Disappointment". The former is from the main characters, after they manage to fulfill the terms they made when they got PCP serialized, and thus avoid cancellation. Miyoshi does this at times, such as when the main characters are first serialized.
In Sailor Moon R, Beruche (Birdie in the DiC dub) is confused when she sees Kōan (Catzi in the dub) crying after she starts her Heel-Face Turn. Beruche, in the dub, asks her why she's crying as they embrace. Kōan tells her, word for word, that they'r tears of joy.
In Tiger & Bunny, Kotetsu cries these when he realizes that Barnaby remembers him again. Karina cries them two episodes later when it turns out that Kotetsu didn't really die.
Happens several times by Nia in Tengen Toppa Gurren Lagann, always when Simon does something special for her. The two most notable occasions are when she was kidnapped, first by Guame and second by the Anti-Spiral. Both times she has a stern, serious look, despite her facing death, confident Simon will rescue her. It's only when Simon finally does rescue her that she finally loses her composure.
Several times in The Idolmaster, most notably in episode 20 when Chihaya just lets the waterworks gush after recovering from all the turmoil inflicted on her.
In Code Geass Suzaku cries with joy when he is reunited with his friends after the hostage-taking incident. In R2, when it is fully brought home to Lelouch how deeply his friends care for him, he has a truly beautiful monologue to himself on the nature of happiness and the few good memories he has, and is moved to tears (though this could be a combination of happy and sad, since he is also thinking of all the loved ones who are not there with them.)
In Hetalia, a sketch by Himaruya shows that whenever Ancient Rome leaves Heaven to check on his grandsons, the eldest grandkid Romano cries these tears. This being Romano, he then hides so his grandpa won't see him cry.
Joe from Ashita no Joe is seen crying quietly after the "welcome back" aprty thrown for him when he returns from juvenile jail.
Season 2 Episode 11 of Black Butler. Alois (in Ciel's Body) asking Hannah to tell him that she loves him and give him a hug. Which he's always needed. She does both, which prompts him to cry tears of joy and say "Love is...warm, isn't it?"
Nagisa in CLANNAD starts crying at the end of the first season, when Tomoya asks her to date him and confesses his love to her at the same time.
Happens in X-Men at Scott and Jean's wedding. At the reception, she saves the last dance for Xavier, which would seem awkward since he's in a wheelchair, but she uses her telekinesis to lift him up and they proceed to share a proper dance. A few of the X-Men shed joyful tears watching them.
Several times in Dragon Age The Crown Of Thorns. Faren,the dwarven commoner, experiences this after he is smacked out of his Fade Demon-induced nightmare. More shocking is when Trian Aeducan, of all people breaks down though.
In Game Theory, Precia sheds these when Alicia finally wakes up.
In Stallionsof Harmony Verse, Blueblood sheds them when he sees the rest of the Stallion Six still alive, and later when he's reunited with Princess Celestia.
When Data finds his cat Spot alive and well after the Enterprise saucer's emergency landing in Star Trek: Generations, he cries, and thinks that his emotion chip is malfunctioning. Troi tells him "I think it's working perfectly."
In one of the Wee Sing live action videos, the following dialogue happens:
B: Why are you crying?
A: I always cry when I'm happy.
B: Well, what do you do when you're sad?
Pepper Potts cried these in Iron Man when she saw Tony when he first came back from being imprisoned for three months.
At the end of Kill Bill Vol. 2, The Bride is seen on a motel room's bathroom floor crying while clutching a stuffed animal. A close-up of her face reveals that these are indeed Tears of Joyat her Happy Ending, with Bill dead and having been reunited with her daughter.
In John C. Wright's The Golden Transcedence, when Helion has paid off Phaethon's debts by way of an apology, and they meet again, Helion offers Phaethon a legal document. Phaethon knocks it aside to embrace his father, and Helion uses the paper to dry his "joy-wet" eyes before remembering to give it to Phaethon, who deeply appreciates it even in its less than pristine state.
In Dan Abnett's Warhammer 40,000Gaunt's Ghosts novel His Last Command, the sight of Gaunt makes Zweil's eyes well up before he declares that it has given him the most joy of anything in his long life.
But Harry had eyes only for the man who stood in the largest portrait directly behind the headmaster's chair. Tears were sliding down from behind the half-moon spectacles into the long silver beard, and the pride and gratitude emanating from him filled Harry with the same balm as phoenix song.
In Teresa Frohock's Miserere: An Autumn Tale, Lucian feels he could shed these after Lindsey rejects Catarina for him — until Catarina resorts to force instead.
From P. G. Wodehouse's Thank You, Jeeves, after Jeeves has bailed the hysterical Bertie out of trouble yet again. Granted, Bertie expresses gratitude towards Jeeves Once an Episode, but this moment is especially significant given that Jeeves quit working for Bertie at the beginning of the book, and Bertie tried to replace him with another valet who just didn't compare:
'Jeeves,' I said, and if there were tears in the eyes, what of it? We Woosters are not afraid to confess honest emotion, 'there is none like you, none.'
In L. Jagi Lamplighter's Prospero Regained, Miranda starts to cry when her siblings take over her duties at Prospero Inc., so she can go off with Astreus and spread the news of their freedom among the elves.
In Jane Austen's Sense and Sensibility, after an entire book of keeping her emotions in and not reacting to anything, when Elinor learns Edward's able to marry her after all, she runs out of the room crying "tears of joy, which she at first thought would never cease."
In the Anne of Green Gables series, Anne explains why she's not a big fan of diamonds and would rather have pearls for her engagement ring. Gilbert points out that pearls symbolize tears, and Anne in turn mentions the several times she cried tears of joy.
In one of the climaxes of Samurai Sentai Shinkenger, Takeru just barely got out alive after a death duel with Juzou, thanks to his friends. When he tried to leave again, since he was actually the clan lord's Body Double and he felt extremely guilty for tricking his friends, all his friends made him listen that they'll always stay by him, even if he's fake, because their experience together aren't fake and he is the 'lord' in their eyes and the lord that they pledged their loyalty to. As an ultimate expression of how glad he is that he still got friends, Takeru had quite the heartful cry.
In the comics we get a new Slayer, Satsu, who was reduced to this due to the events at the end of season seven.
The Doctor Who episode "The Doctor, the Widow and the Wardrobe" has the Doctor repeatedly notice this in other people and remark on how it's a strange human thing: "Happy tears. Humany-wumany". The ending reveals he's full of it when he starts doing it himself.
In the series Legendofthe Seeker, when Cara discovers the kind little creature u pon which the universe's destiny rests, and which she is trying to save and help giving birth after this creature witnessed an horrible event, is dying, she is understandably sad. After laying her on a flower on a place in which the Nightshade (the creature) had to give her babies birth, she turns back and hears a strange sound, while the light lowers around her, and when she turns back again, she sees that her babies have just been born, and fly around, understands that she did not fail, that they are going to live and that she has just saved everyone with them, the usually collected Cara cries tears of joy. Later, she meets the injured Kahlan, help her to climb and begins answering Kahlan's inquiries about the creature' s situation by uttering, with a beam (possibly bordering tears of bliss again), she wishes she (Kahlan) would have been there, because it is the most beautiful thing [she] (Cara) [has] ever seen.
In many game shows, it is not unheard of for a contestant that wins a grand prize (money, a trip, a car, etc.) to break down crying in absolute joy since they won something they could never get on their own.
In The Wind Waker, Orca cries, apparently for the first time in a long while, after Link masters the sword technique he never could.
Zelda cries tears of joy in Skyward Swordafter Demise is defeated.
Groose also sheds these, twice: the first time when Link informs him that Zelda is on the Surface, but she's okay. The second time when Zelda wakes up from her thousand-year sleep, but this time he full-on blubbers like a baby.
Arguably, the most moving example would be the reunion between Zuko and Iroh. Try not to cry yourself, we dare you.
Gus Griswald in Recess during his first episode. He begins crying tears of joy after the other main five gave him a tour of the school and making friends with him, telling them about how in all of the schools he's been at in the past six years, he's never had any friends, and is glad that they're so nice to him.
My Little Pony: Friendship Is Magic: Princess Luna sheds one in "Elements of Harmony" upon being welcomed back by her sister. Pinkie Pie sheds these in "Baby Cakes" upon hearing Pound and Pumpkin Cake's first words: "Pinkie" and "Pie" respectively.
Played for Laughs in "Cartmanland": Cartman does this when he's having the time of his life, completely alone, at his own personal amusement park. "I'm so happy!" *sniff* "I'm so-ho-ho ha-happy-yy!!"
Beetlejuice: In "Doomie's Romance," Lydia cries happily when Doomie's tears revive Pinky, the Mayor's former pink convertible. Beetlejuice does so as well, but he uses the old excuse that he had something in his eye.