Kefka (already mentioned) and Sephiroth - their evilness is presented as a matter of insanity. (And for all I'm a Final Fantasy fan, I'm well aware of how problematic that is.) FWIW, Kefka was also described as "autistic" in an official(-ish?) book, though I chalk that up to the writers not knowing what they were talking about - whatever's the matter with Kefka doesn't bear much (if any) resemblance to real life autism.
On that note, I could rant about how often fictional characters suffer from some not-clearly-defined-but-dramatic "insanity" (which is actually a legal term, not a medical one!), whether presented as matter of evilness or tragedy (or both), rather than any of the distinct psychiatric illnesses that exist in the real world.
OTOH, Cloud (from the same game as Sephiroth) serves as a subversion of that trope - his mind is very, very broken (he's also in a wheelchair at one point in the game), but in the end he's a hero rather than evil. You could consider him the contrasting counterpart to Sephiroth, the way Barret and Dyne (I'll get to them) are presented as contrasting conterparts.
physical impairment examples:
the albino assassin from The Da Vinci Code, though he's not presented as vision impaired or otherwise affected by his albinism in ways beyond looks
More Final Fantasy examples (not always sure where to file them):
In Final Fantasy XI (the online one), the NPC Curilla is missing an eye, though that's not readily apparent (she's hiding the scar under her bangs - yes, the "female characters are not allowed to be visibly disfigured" trope). In spite of this, and partially because of this, she's still an excellent swordfighter - when you finish the Savage Blade quest, she explains it in terms of how she kept training until she'd learned to work around her impairment and "understand the heart of her foe." So I guess trope-wise, she's falls partly under Disability Superpower, partly under Plucky And Inspiring, with a side dish of Martial Artist Whose Intuition Is So Finely Honed That They Can Fight Blindfolded. There are also some Unfortunate Implications in the story of how she got that injury (namely, during a swordfighting tournament, i.e. in the course of being competitive while female).
In the same game, Eald'narche and Gilgamesh wear eyepatches, though Eald'narche's is more a case of "something to hide" than disability. Chieftainess Perih Vashai is fully blind, with shades of the "Blind Seer" archetype - she may no longer be able to shoot a bow herself, but she's still the wise woman whose tests an aspiring Ranger must pass. An NPC near her explains that she keeps her eyes closed so she can see better on the spiritual level or something along those lines, though I thiiiiiink it's also that she did something during the Crystal War that killed her eyesight as a side effect (can't give you the details since I'm not done catching up on the Windurst Wings of the Goddess quests, nor have all of those quests been released yet).
Still on Final Fantasy XI, that game is also an example of "Wookies need extra legroom" handled well (if by "well" you mean "non-anthropocentric"). There's the Galka that are much taller than humans and have a tail, the Elvaan than are taller than humans with long necks, the Tarutaru that are much smaller than humans, the Mithra that are somewhat smaller than humans and also have a tail - and they all have it equally easy to find armour than fits them. (Though, granted, furniture is more or less scaled to human proportions unless explicitly made for Tarutaru.)
Final Fantasy VII has Barret and Dyne, who both have a prostetic arm that doubles as a machine gun. Dyne (once Barret's best friend) is presented as driven to evil by what happened to him (we meet him after he went on a murder spree) - a case of the Monster (and possibly More Machine Than Man) trope. Barret is his contrasting counterpart - while he is an ecoterrorist when we first meet him, his personality is mostly "good person under the gruff exterior" and "caring father."
In regards with his prostetic, for all the cool factor of it, I can't help thinking about how he dealt with it in daily life - a gun arm may be useful in battle, but what about dressing oneself? Washing dishes? Hugging one's little daughter? (Advent Children actually came up with a solution, showing him with a more conventional prostetic limb that could be transformed into a gun for combat purposes.)
Also from Final Fantasy VII, there's Vincent with his golden claw. While it's never explained in-game whether it's a prostetic or a piece of armour, it's commonly assumed in fandom that Vincent's flesh-and-blood arm is either missing or severely disfigured. His monster transformations could be seen as a "disability not existing in the real world" of the Cursed With Awesome variety.
Final Fantasy VII's spinoff Dirge of Cerberus has Shalua, whose most apparent impairments are a missing eye an a prostetic arm, though it's also stated in-game that "more than half her organs have been reconstructed." However, sadly enough, we are told about more than shown her disability - for all that she's supposedly suffering and in constant pain, we don't really get to see her being affected by her impairments (flawless knife fight despite lack of depth perception, anyone?) Then she Tragically Sacrifices Herself and spends the remainder of the game in a life-support pod (which is eventually destroyed, presumably resulting in her death).
Shalua's sister Shelke is a case of "disability not existing in the real world" - she doesn't age (not as awesome as it sounds, since she's stuck with the body of a child), but needs daily Mako treatments to stay alive (the equivalent of a diabetic needing his insulin?); and mentally/emotionally, she is (in her own words) "a shadow of [her] original self" due to her time in Deepground.
Characters in wheelchairs - aside from Cloud (temporarily), there is Rufus Shinra in Advent Children. (Yes, he stands up during a climatic moment, but being able to stand for an amount of time doesn't necessarily equal "not disabled" or "not really needing a wheelchair.") Ironically, he's the opposite of the Evil Paraplegic trope - he was a villain in the original game, when he was able-bodied, and found redemption (sort of) after his run-in with Diamond WEAPON.
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Some examples/additions I could think of
mental illness examples:
Kefka (already mentioned) and Sephiroth - their evilness is presented as a matter of insanity. (And for all I'm a Final Fantasy fan, I'm well aware of how problematic that is.) FWIW, Kefka was also described as "autistic" in an official(-ish?) book, though I chalk that up to the writers not knowing what they were talking about - whatever's the matter with Kefka doesn't bear much (if any) resemblance to real life autism.
On that note, I could rant about how often fictional characters suffer from some not-clearly-defined-but-dramatic "insanity" (which is actually a legal term, not a medical one!), whether presented as matter of evilness or tragedy (or both), rather than any of the distinct psychiatric illnesses that exist in the real world.
OTOH, Cloud (from the same game as Sephiroth) serves as a subversion of that trope - his mind is very, very broken (he's also in a wheelchair at one point in the game), but in the end he's a hero rather than evil. You could consider him the contrasting counterpart to Sephiroth, the way Barret and Dyne (I'll get to them) are presented as contrasting conterparts.
physical impairment examples:
the albino assassin from The Da Vinci Code, though he's not presented as vision impaired or otherwise affected by his albinism in ways beyond looks
More Final Fantasy examples (not always sure where to file them):
In Final Fantasy XI (the online one), the NPC Curilla is missing an eye, though that's not readily apparent (she's hiding the scar under her bangs - yes, the "female characters are not allowed to be visibly disfigured" trope). In spite of this, and partially because of this, she's still an excellent swordfighter - when you finish the Savage Blade quest, she explains it in terms of how she kept training until she'd learned to work around her impairment and "understand the heart of her foe." So I guess trope-wise, she's falls partly under Disability Superpower, partly under Plucky And Inspiring, with a side dish of Martial Artist Whose Intuition Is So Finely Honed That They Can Fight Blindfolded. There are also some Unfortunate Implications in the story of how she got that injury (namely, during a swordfighting tournament, i.e. in the course of being competitive while female).
In the same game, Eald'narche and Gilgamesh wear eyepatches, though Eald'narche's is more a case of "something to hide" than disability. Chieftainess Perih Vashai is fully blind, with shades of the "Blind Seer" archetype - she may no longer be able to shoot a bow herself, but she's still the wise woman whose tests an aspiring Ranger must pass. An NPC near her explains that she keeps her eyes closed so she can see better on the spiritual level or something along those lines, though I thiiiiiink it's also that she did something during the Crystal War that killed her eyesight as a side effect (can't give you the details since I'm not done catching up on the Windurst Wings of the Goddess quests, nor have all of those quests been released yet).
Still on Final Fantasy XI, that game is also an example of "Wookies need extra legroom" handled well (if by "well" you mean "non-anthropocentric"). There's the Galka that are much taller than humans and have a tail, the Elvaan than are taller than humans with long necks, the Tarutaru that are much smaller than humans, the Mithra that are somewhat smaller than humans and also have a tail - and they all have it equally easy to find armour than fits them. (Though, granted, furniture is more or less scaled to human proportions unless explicitly made for Tarutaru.)
Final Fantasy VII has Barret and Dyne, who both have a prostetic arm that doubles as a machine gun. Dyne (once Barret's best friend) is presented as driven to evil by what happened to him (we meet him after he went on a murder spree) - a case of the Monster (and possibly More Machine Than Man) trope. Barret is his contrasting counterpart - while he is an ecoterrorist when we first meet him, his personality is mostly "good person under the gruff exterior" and "caring father."
In regards with his prostetic, for all the cool factor of it, I can't help thinking about how he dealt with it in daily life - a gun arm may be useful in battle, but what about dressing oneself? Washing dishes? Hugging one's little daughter? (Advent Children actually came up with a solution, showing him with a more conventional prostetic limb that could be transformed into a gun for combat purposes.)
Also from Final Fantasy VII, there's Vincent with his golden claw. While it's never explained in-game whether it's a prostetic or a piece of armour, it's commonly assumed in fandom that Vincent's flesh-and-blood arm is either missing or severely disfigured. His monster transformations could be seen as a "disability not existing in the real world" of the Cursed With Awesome variety.
Final Fantasy VII's spinoff Dirge of Cerberus has Shalua, whose most apparent impairments are a missing eye an a prostetic arm, though it's also stated in-game that "more than half her organs have been reconstructed." However, sadly enough, we are told about more than shown her disability - for all that she's supposedly suffering and in constant pain, we don't really get to see her being affected by her impairments (flawless knife fight despite lack of depth perception, anyone?) Then she Tragically Sacrifices Herself and spends the remainder of the game in a life-support pod (which is eventually destroyed, presumably resulting in her death).
Shalua's sister Shelke is a case of "disability not existing in the real world" - she doesn't age (not as awesome as it sounds, since she's stuck with the body of a child), but needs daily Mako treatments to stay alive (the equivalent of a diabetic needing his insulin?); and mentally/emotionally, she is (in her own words) "a shadow of [her] original self" due to her time in Deepground.
Characters in wheelchairs - aside from Cloud (temporarily), there is Rufus Shinra in Advent Children. (Yes, he stands up during a climatic moment, but being able to stand for an amount of time doesn't necessarily equal "not disabled" or "not really needing a wheelchair.") Ironically, he's the opposite of the Evil Paraplegic trope - he was a villain in the original game, when he was able-bodied, and found redemption (sort of) after his run-in with Diamond WEAPON.