1) Know what the disability looks like even if you don't describe it to the reader immediately. Sometimes this is a simple matter of terminology. The author says "eye" at one point and "eyes" at another, leaving me unsure if the character has really lost an eye or was just turned a certain way the first time. It's very easy to forget and pluralize words like hands, eyes, arms, feet, legs, and so on when you have a character who's lost a paired part of his body. Do go through and root them out, though, because it can confuse your readers.
Other times, the slippage is more severe. The author claims at one point that the character lost a hand, and at another that he lost an arm. Well, which is it? Such things do make a difference, especially if the character is trying to maneuver around ordinary life immediately after the injury (see point 2). Similar things happen with a foot and a leg. This is one of those pesky times when you have to remember that, even if the people in your fantasy book are speaking a language other than English, your readers are reading it in English, or another Earth language. Your characters might not make any differentiation between a hand and an arm, but that nicety has to be sacrificed.
If the injury doesn't involve the loss of a limb or eye, then it can be harder to picture. Say the character's "paralyzed from the waist down." Yet later in the book, the author shows her tapping her foot to music. Huh? The author needs to hold the disability very firmly in her own mind, and if she provides what are two completely different pictures on the surface, they had better be cleared up, and soon.
2) Remember that a disability makes small, ordinary tasks hard, as well as greater skills. The focus in fantasy is often on "skills"- what the character can do as far as fighting or magic goes. (At some point there shall be a rant on why this is too often simplistic). So the hero who loses a hand is pitied because he'll have to relearn the sword, or the mage who goes blind immediately thinks first of how she can't read her spellbooks anymore.
Y'know, the first thing I'd wonder about if I lost a hand would be how I was going to dress myself, not about how I was going to fight. And then would come carrying things around. And then, maybe, fighting. Similarly, the mage is going to have a whole host of problems that have nothing to do with losing part of her magic. It might be a big thing, but it should not be the only thing.
This is where the exact extent of the disability becomes important. Is the character absolutely stone blind, can't see anything? That's different from a character who's mostly blind but can still, say, make out sunlight if she turns her head in the right direction, and perhaps faint silhouettes. A character who lost a hand but still has his arm could use that arm to balance things against his chest while opening a door with his hand, while someone whose arm is gone at the elbow or higher will have it much harder.
If some of the problems don't seem obvious, do a little research. Consider how difficult it would be to get around in a seeing people's world if you've just been struck blind. (It would be worse, not better, in a fantasy world, unless they had extremely specialized magic). Try tying one hand behind your back and see how it affects your daily life. The newly disabled character has a lot more to get used than just the loss of a skill.
3) If you want a natural phenomenon or a disease to cause the disability, make sure it can. This means that if you're not sure, look it up. Frostbite can cost someone his ears, his fingers, his toes, and other parts of his body, but that's because it's frostbite. Merely walking through a day that's about 50 degrees Fahrenheit/10 degrees Celsius for two minutes is not going to give a normal human frostbite. Also, cholera does not cause blindness, sorry. (Untreated scarlet fever can). Lightning can charbroil someone pretty well, but I have yet to hear of it giving anyone DID. Sometimes the explanations for the disabilities become too far-fetched to believe.
This applies to magic too, actually. If a curse causes blindness in everyone else, but deafness in the heroine, why is she different? "Because I want her to be" is not good enough. It could become the core of an intriguing novel, but eventually an answer would have to show up.
4) Don't use the disability as an excuse to make your hero "better" in some way. I hate to death those fantasies where the hero loses a hand, and about a chapter later, he has a magical special silver one that's stronger than any ordinary human hand and can grip a sword better and gives him the ability to shoot lightning bolts. It starts looking as though the author took away his hand only to provide a little shallow angst- maybe not even that- and then an excuse to give him something better.
If the point of the story is going to be the hero adapting to what happened to him, or what he was born with, and eventually overcoming it with the help of magic or a quest or whatever, then do make that the point of the story. Show what he learns along the way, the subtler adaptations that go with the magical help, and why, by the time he gets the magical help, he truly has earned it. So your heroine goes blind, but the mages quickly train a seeing raven for her and give it to her, and the raven is telepathic and funny and obeys her perfectly and even gives her eyesight better than human? I'm sorry, why did she go blind again? What's the point? You could have a sighted heroine with a telepathic talking raven whose eyes she could share, and it would be more honest.
This is why so much suffering in fantasy books annoys me so. It's not suffering. It's only something that could have tragic consequences happening, and the author promptly averting any and all tragic consequences. It's an orgy of angst and specialness.
Speaking of that...
5) Give your character other things to worry about beyond the disability itself. This is a distinction that seems lost on a lot of authors, but it's the same as a difference between a struggle to adapt and a simple method of adapting that winds up making the hero's life better than it was before. If his disability is severe enough- say, deafness and blindness both at once- it's not only going to affect his sight and hearing. It's going to affect his relationships with other people, the way he physically moves, his livelihood, his ability to perform lesser "skills" like reading, his safety, and on and on and on. Given all this rich palette of angst, the fact that an author can choose to have the character repeat, over and over again, that he misses colors or music simply astounds me.
If the disability is not that severe, then for gods' sake stick the character in the middle of a worrisome situation made harder by the disability in some way. Don't make the disability the core of the story. There is life after losing a hand, and it's a hell of a lot easier than it is for a character who's suddenly been stricken blind and deaf. If your hero has to worry about saving the world, when he was supposed to fight a duel to the death, and now that he's lost a hand he can't really do that, there's a legitimate reason for moments of shock and times of frantic training. But if his life is otherwise good and he has only that to moan and groan about, the story very quickly becomes boring.
6) Portray the reactions of people who don't know about the disability reasonably. Shall I now mention one of my most hated plotlines in fantasy? Yes, I shall.
You have a character who has a disability, one that's not immediately visible. We shall say she's a heroine with hemophilia. She doesn't choose to tell anyone about it unless she has no choice, because she's a private person, and embarrassed about it. Her traveling companion, who doesn't know, tosses her a knife to cut their food up, and she slices her hand on it and nearly bleeds to death. Then she rants at him for not knowing, and usually gives him the silent treatment, utterly ignoring any attempt to apologize (probably until she notices the hero is attractive). The hero has to grovel, and the author paints him as an insensitive cad for not knowing already.
Is this reasonable? Is this rational? I don't think so. It requires that the hero somehow be a mind-reader, when most of them aren't telepathic. It would be one thing if the author eventually had the heroine explain her reasons, and treated it as a mistake, but it's almost always treated as though the hero made a deliberate attempt to offend or kill the person with the hidden disability.
Fuck that. It's another Big Misunderstanding Plot waiting to happen, where one character should somehow have guessed a silent character's thoughts, and I think you all know how I feel about those.
7) Realize that a disability by itself does not make a character. "She's blonde and blind" is no more a complete character than "She's blonde and can perform great fire magic" is. Try to construct a story that flows from the character interacting with other characters, the setting, and the plot, not just, "Oh, but she's blind!!!!" Just changing one part of the normal fantasy story doesn't make it different. It looks too much like a gimmick. Deep-reaching changes in the way that you employ old fantasy methods, or deep-reaching changes in more than one aspect of the archetypes, are what's needed.