Setsumi in Narcissu has an unnamed condition. She kills herself at the end of the story.
Miku in A Profile as a result of a slightly botched liver transplant.
Toko in Kara no Shoujo is anemic and spends a lot of time sleeping. She also requires some special medicine. All in all, though, it's not too bad until Mizuhara thinks it's some sort of drug, steals it and Toko ends up getting hit by a truck when she passes out.
Ever17 features two: Yubiseiharukana (the You from Takeshi's path) who has a terminal heart condition and Coco Yagami who has Tief Blau.
In the "Heaven's Feel" arc, Sakura is revealed to be this, due to the stress of the Matou family's crest worms becoming more active. Shirou has a treatment for her, at least temporarily.
Additional materials reveal the existence of another ill girl: Kirei Kotomine's dead wife, Claudia Hortensia, an inmuno-deficient Mysterious Waif who passed away two/three years after they got hitched. (In a subversion, she actually commited suicide in a desperate gambit to prove him that he wasn't as unfeeling as he thought — then again, Claudia was already dying so she wouldn't have lasted much longer anyway).
Miyu Shizuhara from Crescendo. Her illness isn't specified, but it requires her to stay at the hospital for a good part of her route. And she does NOT get better.
All the main girls in Katawa Shoujo; in fact, the game started out as an attempt by The Image Board That Must Not Be Named to create the videogame with the highest Ill Girl count possible. Though ironically enough, only the male protagonist's condition is actually life-threatening, since the heroines are all in some way physically disabled but otherwise healthy. There is one Ill Girl that plays this trope straight: Saki Enomoto from the Aprils Fool "Event", whose disease (spinocerebellar ataxia) will eventually kill her.
The eponymous Kana from Kana: Little Sister. The cause of her disease is clearly stated: kidney failure. The game also features Sumako and Cana. Two of the three die.
CLANNAD has Nagisa (unnamed illness that may have supernatural origins) , Fuko (is in a coma after an accident), and Ushio (her mom Nagisa's same illness)
AIR has Misuzu, whose illness is actually born from a curse.
Planetarian has Reverie/Yumemi, with low battery power and unable to recharge due to planetarium's backup power supply failure just after the show, and that they're stuck in post-apocalypic Earth.
Yuzuha in Utawarerumono, who is actually something of a MacGuffin - her brother Oboro's theft of the outrageously expensive medicine she needs to survive is the start of a chain of events which snowball into an international war.
Ange also was one when she was younger, as being afflicted with a severe cold is what preventing her from going to the 1986 family conference. She was also noted to often be sick aside from that instance.
Played with in ef - a fairy tale of the two.: Chihiro Shindou doesn't spend almost any time bedridden or hospitalized, but she still suffers the serious consequences of having been hit by a car three years prior to the story ( the loss of an eye that she covers with a white eyepatch, and retrograde amnesia that takes effect every 13 hours), so she requires to be taken care of. In short: Chihiro is an Ill Girl turning into a Bandage Babe when she got better.
Another Chihiro with a bad health is Chihiro Fujisaki from Dangan Ronpa, who never had the strength to go out and play with others as a little girl. Except Chihiro is an ill boy, not an ill girl, and one of the reasons why he crossdressed was because he was considered "too weak" as a boy and was bullied for it, so he tried to protect himself via crossdressing. And we don't find out until we find him dead.
In Super Dangan Ronpa 2, there's Teruteru Hanamura's mother, who had worked herself to illness and exhaustion to keep the family restaurant open. Teruteru worries a lot about her health, and his desire to get off the island to find out if she's alright eventually drives him to murder.
Da Capo II: There is a double example in one route: Anzu. Said girl was the first to fall ill, then comes the protagonist boy's turn. They both spoon spoonfeed soup to each other when the other one lies sick in bed.
Viola Cadaverini from Ace Attorney looks like one given her pale and creepy/sickly appearance as well as the bandage on her head. She's a bit of a subversion though since the bandage is due to an injury that she got in a massive accident caused by her sort-of love interest Furio Tigre and it is implied that she is just a frail woman by physical nature, not illness.
Male lead Hisao. While the girls are physically disabled but otherwise fine, he's got severeheart arrhythmia that almost kills him in the introduction. It doesn't do him any favors when Emi runs into him in the hallway, either, and keeps being a problem over the course of the game. Especially in Lilly's route, in which he has two major incidents... and a third on the way to the Good Ending that hospitalizes him again and almost kills him.
Kenji Setou, who not only is legally blind but is speculated to be mentally ill as well. Only that he's a Large HamConspiracy Theorist instead.
Shiki Tohno from Tsukihime fits into the role in two different respects. The accident that didn't quite kill him still left him with poor health and occasionally life-threatening anemic attacks. On a more subtle but drastic level, his Mystic Eyes of Death Perception growing constantly stronger means his lifespan is cut extremely short, and he's likely to die before long when his brain overloads.
In Super Dangan Ronpa 2, Nagito Komaeda is apparently this, specifically having dementia and stage three malignant lymphoma, and it's implied that his illnesses were what turned his hair white. While in the game it's unclear whether or not he's actually telling the truth about having these illnesses, supplementary materials have supported his claims.
Although Key Visual Arts is well-known for its ill girls (see above), Little Busters has two male examples and no real female examples, as while Mio is very delicate and seems sickly at first, her issues are very different. Most obviously there's Riki, the very Moe protagonist, who suffers from narcolepsy. And secondly there's Komari's older brother, who suffered a deadly disease that killed him when Komari was only a small child.
And Ryou's Second Love Kappei Hiiragi from CLANNAD, who has bone cancer. He either has to get his leg amputated or die.