Special needs middle grade fiction?

I'm not sure it's classified as MG (I'm pretty sure it isn't), but maybe Tortuga by Rudolfo Anaya.

Flowers for Algernon?

Definitely Flowers for Algernon, and perhaps you should look at Of Mice and Men.

The Thing About Georgie, by Lisa Graff, is about a dwarf. Not a disability, but a distinction that makes him different. It's not written in the first person, though. You can check out the first pages on Amazon, to see if it's something that might help.

AL CAPONE DOES MY SHIRTS has a character with pretty severe autism, set in an age when no support was in place for families. It isn't written from her perspective, though, but from the younger brother's.

I loved Al Capone Does My Shirts.

Also check out Wild Orchid, by Beverley Brenna, which is told in the first person voice of a girl with Asperger's. It may be YA rather than MG but it is well done and worth reading. Also Hurt Go Happy by Ginny Rorby is an MG novel told from the POV of a deaf girl who has not been allowed to learn sign language-- haven't read it yet, it's in my to read pile.

"The Acorn People" by Ron Jones is a MG novel written from the perspective of a camp counselor for kids with severe disabilities, but it's still worth looking into. I think it's a really gritty and sensitive look at the lives of the kids...it's much more about the campers than than the counselor. Also I freakin love this book.

Accidents of Nature by Harriet McBride Johnson--about a girl with CP going to camp with a bunch of other kids with disabilities (the author had muscular dystrophy I believe)

Tangerine by Edward Bloor-about a legally blind kid who plays soccer

the Joey Pigza books by Jack Gantos--about a kid with ADD having various everyday adventures

then of course there is Percy Jackson and the Olympians series by Rick Riordan, about a kid with ADHD who has to fight evil creatures from greek mythology

The Thing About Georgie by Lisa Graff--about a kid who's a dwarf

Stuck in Neutral by Terry Trueman--about a kid with severe CP who cannot communicate

If you would read some YA, "Head Case" by Sara ARonson (quadriplegia) and "Marcelo in the Real World" by Francisco Stork (Aspergers Syndrome) are some recent ones.

LOSER by Jerry Spinelli--he doesn't say the character has Asperger's, but I'd say he's on the spectrum. He's quirky, anyway, with limited social skills, but by the end he finds a place in the group.