It's tough being an orphan. No parents, no home and a large chance you'll be placed in the horrible Orphanage of Fear. But some fictional orphans get lucky, and go to the Orphanage of Love instead.
At the Orphanage of Love, there's enough food for all, and it tastes good. The rooms are spacious and well lit, the beds are soft and laundry is done frequently. The staff genuinely care about their charges and competently take care of them until good foster homes can be found for their precious angels. (Because no matter how wonderful the Orphanage of Love is, actual parents are even better.)
Mind you, employee screening isn't perfect, and sometimes a Child Hater will somehow get on the staff and abuse the orphans until he can be exposed. Also, money is generally in short supply, so the heroes will often have to raise a bundle of cash to keep the place running or avoid having it foreclosed on by a Dastardly Whiplash land developer. Expect the heroes of the story to try Saving The Orphanage through whatever wacky means necessary.
Same to the one Nadja lived in at the beginning of Ashita no Nadja. When Miss Applefield dies in an accident, however, it's dismantled.
The Maxwell Church from Gundam Wing was very poor, but otherwise it did well and was run by the kind Father Maxwell and his assistant Sister Helen. Pity it was blown up in the war and the only survivor, Duo, was quite traumatised.
Dee from FAKE was raised in an orphanage like this, It was nearly destroyed by a developer who wished to build on it and the orphanage's owner who raised Dee, a nun, is nearly killed.
Hana No Ko Lunlun has the heroine running across one in the South Italian countryside (not exactly mentioned where in Italy, but considering she had just left Sicily, it could be anywhere in Calabria), run by a nun named Sister Mariana and with kids from the age range of 5 to 15. The eldest children, lead by the Hot Blooded Emilio, also fret over cute little Lucero's Ill Girl condition and desperately seek for the money they need for her operation, so they're overjoyed when there are rumors about a hidden treasure coming from World War II. It wasn't a treasure... but an old bomb.
Najika of Kitchen Princess had one of these in the Lavender House, which the director of her school tried to shut down, in order to blackmail Najika into losing a cooking contest. It didn't work.
It's implied that Father Andersong is the head of one of these in Hellsing (though, since a lot of these orphans then go on to become part of the Church Militant, the reader may not consider it to be a good place to grow up).
In Mirai Nikki the orphanage that the 8th runs seems to be one of these, considering how far her kids go to protect her. And she seems willing to fight for the sake of the kids as well.
Kabuto of Naruto ended up in one after his original home was destroyed in a war and he lost his memory. While by no means perfect, the children and one of the caretakers accepted him as family. Even years since last seeing them, his fellow orphans think of him as a brother. Also offers a much grimmer example of protecting it from closure. While still a child, Kabuto became a spy for Konoha to prevent Danzo shutting off the aid.
While not an actual orphanage, the majority of the wizards in the title guild of Fairy Tail are teens or young adults without family ties, who have come to look at the guild as their family. A lot of them have even been there since they were small children.
In Saint Seiya, the title character and his older sister Seika spent some time in one of these before Seiya was forcibly taken in by the Kido Fundation and Seika disappeared in search of him. It's featured once in a while since Seiya's Unlucky Childhood Friend Miho still lives and works in it, so in his (almost nonexistant) free time Seiya tends to hang out there, sometimes with Saori and the other Saints joining him. This is a plot point in one of the non-serial movies: Eri, the other worker at said orphanage, turns out to be the Soul Jar for Eris the Gddes of Revenge.
The Belgium comic book series Orphanimo! is all about an orphanage of love. The last 5 orphans living there love the place and it's owner so much, they sabotage every attempt of the owner to find them adoptive parents. A rich and powerfull industrial however wants to buy the orphanage to use the ground for his latest building. The orphans, of course, try to prevent this in every way possible.
While it was pretty dickish of Superman to put his cousin Supergirl in an orphanage after her arrival in the Silver Age, at least he cared enough to make sure it was a really nice one.
For Superman himself, the Smallville Orphanage (where the Kents left him at, before returning to formally adopt him) was usually also shown as such.
In the New52 reboot of Batman, this continuity's Owlman Bruce Wayne's brother Thomas Wayne Junior was seriously injured in his youth and sent to a prominent children's hospital by his parents Thomas and Martha Wayne to recover in secret. Thanks to the Waynes' funding, the hospital fit this trope. Sadly, when they were killed the funding dried up and the hospital became an Orphanage of Fear. Owlman wants revenge on Bruce for their parents' deaths which lead directly to his life becoming a living hell.
"In an old house in Paris, all covered in vines, lived twelve little girls, in two straight lines". The smallest one was Madeline. Though it's technically a boarding school, Madeline herself is an orphan and the other kids' parents never really figure into the plot.
Plumfield Estate School, the orphanage/school that Jo and her husband run in Louisa May Alcott's Little Men.
In Jane Eyre, Jane gets sent off to Lowood - a boarding school that is basically for orphans and poor children - which goes from an Orphanage of Fear to Orphanage of Love over time.
The orphanage in which Voldemort grew up is more or less described as a pleasant, if gloomy, place to be raised — Tom Riddle himself was the problem.
From a certain point of view, Hogwarts itself could be seen as one of these as far as several students are concerned. Which makes it all the worse in the seventh book when the school is run by Death Eaters.
Harry realizes that this is one more thing he has in common with Voldemort and Snape. All three were lost boys who found a home in Hogwarts. Even Voldemort is uncharacteristically sentimental about the place.
Jean Webster's book Dear Enemy is composed of letters written to various people about the goings-on after the heroine takes on the responsibility of an orphanage, which used to border on Orphanage of Fear until she came along. The "Enemy" of the title is the doctor with whom the heroine cannot get along (for most of the book, at least). The orphanage suffers from a lack of staff and money, but at least manages to get some community support when a fire burns the place down and the orphanages get sheltered with various townsfolk for a while.
The orphanage in Adopt-A-Ghost certainly applies, to the point at which the children love the matron and other orphans so much that they try to avoid being adopted if possible..
Which Witch?, at the end when the old matron-turned spider is replaced by a sweeter woman.
The orphanage/boarding school Georgie is sent to in The Lottery Rose would qualify.
In Brat Farrar by Josephine Tey, the protagonist's backstory features such an orphanage:
It was a very good orphanage; a great deal happier than many a home he had seen in passing since. The children had loved it. They had wept when they left and had come back for visits; they had sent contributions to the funds; they had invited the staff to their marriages, and brought their subsequent children for the matron's approval. There was never a day when some old girl or boy was not cluttering up the front door.
Mother Karen's home in Spellbent and Shotgun Sorceress by Lucy Snyder is one of these. Mother Karen herself rivals Fred Rogers in the "Friend to all children" category and is unfailingly kind even when monumentally stressed out. What she can't do, she relies on the teenage orphans (raised under her sterling example, of course) to do.
In John C. Wright's Chronicles Of Chaos, the boarding school stradles the line between this and Orphanage of Fear. On the one hand, they are treated affectionately and given an excellent education. On the other hand, the teachers are under orders to kill them if they start remembering things.
The foundling hall in Michelle Sagara's Chronicles Of Elantra is run by a caring and fiercely protective Leontine woman who treats the orphans as her own and does everything she can to keep them well fed, well clothed, and well educated.
Natalie Savage Carlson's twenty Orphelines lived happily in a small private orphanage run by Mme. Flattot and her assistant Genevieve. There were several books about these little girls, who regarded themselves as a family and didn't want to be adopted.
Downplayed in Steve Berry's The Third Secret. The Romanian orphanage is... a Romanian orphanage. But the nuns and priest who run it are very kind. There just isn't enough money. Fr. Tibor's holding the place together with Scotch tape and rosary beads before he's murdered. But Fr. Colin is inspired to make the orphanage his life's mission, and he's bringing his considerable personal fortune with him.
In Sharpe's Prey, the orphanage at which Astrid works is this. Sharpe, who grew up in an Orphanage of Fear, takes a while to actually understand the concept.
In the Champions supplement Allies, the tokusatsu-inspired Zen Team operates out of such an orphanage as part of their cover. The children weren't fooled for long.
The entire playable party (plus Seifer, minus Rinoa) in Final Fantasy VIII grew up in one. GF-induced amnesia made everyone except Irvine forget.
Milla Vodello in Psychonauts has a backstory where she worked in one of these. Until the orphans tragically died in a fire, an event that haunts her subconscious to this day.
Jade from Beyond Good And Evil operates her Lighthouse Shelter, specifically for war orphans. They run a little low on cash sometimes, but there's warm beds, plenty of food, a Big Friendly Dog, and, you know—lighthouses are inherently cool.
The third world in Mystic Ark could essentially be summed up as this ( Even though they never had parents to begin with and Cecille (the caretaker) created everything from the ground up with the help of the Wisdom Ark), though for a good half of the time you spend in that world, Chimera, influencing Cecile, turns it into the opposite, especially during the final part of your visit there when the orphanage is overrun by monsters.
In MS Saga, the hero and his cowardly sidekick were raised in one, complete with the kind, matronly caretaker. Of course, this being Gundam-related, it gets attacked by Zakus and burned down with everyone but the two of them inside.
In World of Warcraft both the horde and the alliance both have an orphanage in their capital cities for children who lost their parents due to the war. Both are run by caring and loving women, and they all seem to have lots of fun there. And once a week every year they host a holiday event whee players take a kid on a world wide trip to give them a perfect day out.
Unfortunately, the Lord British Postulate extends to these kindly matrons. When they relocate to take their charges trick-or-treating, some of the less desirable elements may target the matrons.
Hanako Ikezawa from Katawa Shoujo lived there until she came to Yamaku. There's somewhat of a subversion, though: while the staff treated Hanako kindly and she was kind of a Parental Substitute for the youngest children in her last days there, she still couldn't make friends.
In the backstory of Jade Empire, there was one in Tien's Landing. The monstrous Emperor decided to flood the town while the orphan-keeper was out buying food. He tried to save his orphans, but failed to get them all out. Ten years later, the ghosts of the orphans want peace and the old man is still beating himself up and drowning his sorrows at the tavern over his failure. Your Spirit Monk can allow him to be killed by the angry ghosts, or earn a heartwarming moment by allowing the old man to make amends by giving the tots a proper burial.
In Fire Emblem Awakening, Libra the War Monk builds and mantains one of these in all of his endings note Save the one with a girl Avatar, since those are generic. If he's married, his wife (and presumably their child) will help him out take care of the orphans — with different results, depending on who she is.
The title character of Selkie was adopted from one, and it continues to be an important setting throughout the story.
The orphanage in Meet the Robinsons where Lewis and Goob grow up appears to be one of these, complete with kindly matron Mildred.
Interestingly, the DVD commentary says that Mildred is careful to not coddle the children too much since they need to be able to leave when adopted without emotional hang-ups. The biggest problem at Lewis' orphanage is, well, Lewis himself, though he gets better.
Foster's Home for Imaginary Friends, but with imaginary friends whose owners have grown-up and left them. It has a surprisingly very very very small staff for such a one-of-a-kind place, but everyone there generally enjoys their stay.
Mr. Harriman and Mrs. Foster are essentially administrators. Many of the orphaned friends do a lot of work to keep the place running, though Frankie has to take up the slack.
The orphanage where Tim lives in Nocturna doesn't really feature too much in the movie, but it appears to be more or less this trope; children are given the run of the place during the daylight hours and there are plenty of toys to keep them amused. The only hitch is that Tim tends to be given rather a rough time by the other children because of his noisy bedtime ritual.
The first Care Bears movie has its framing device Mister Cherrywood telling a bedtime story to kid at an orphanage. From what little we see of it, the children seem to love the staff.
Cookieville Minimum Security Orphanage from Futurama is as close as it gets to this trope, operating in a Crapsack World on a shoestring budget. All of Leela's memories of the place are good (save for the teasing about her eye), the director genuinely cares about the kids and he generally works hard on making them happy and finding them new parents.
The Children's Home in Warsaw run by Janusz Korczak appears to have been this. The children had their own court, they were treated fairly, and the two heads worried themselves silly if a child refused to eat. The director even sacrificed his own safety to go with the children when they were shipped off to be murdered in a concentration camp, despite offers from friends to hide and shelter him. (Of course, they didn't have room for 100 children, so he made his choice.)