Dean with a severely injured leg:
Holding the Sky by reapertownusa
http://archiveofourown.org/works/937001?view_full_work=true (http://archiveofourown.org/works/937001?view_full_work=true)

Dean with an amputated leg:
Where Do We Begin (The Rubble or Our Sins?) by dimeliora
http://archiveofourown.org/works/1025195?view_full_work=true (http://archiveofourown.org/works/1025195?view_full_work=true)

Dean is deaf and blind:
Dark Side of the Moon by fleshflutter
http://fleshflutter.livejournal.com/11169.htm (http://fleshflutter.livejournal.com/11169.htm)

Mute Sam and Blind Dean:
Thousand Verse by saucyminx
http://archiveofourown.org/works/59465?view_full_work=true (http://archiveofourown.org/works/59465?view_full_work=true)

Blind and Deaf Dean:
The Year of Letting Go by runedgirl
http://runedgirl.livejournal.com/32053.html (http://runedgirl.livejournal.com/32053.html)

There are also several great recs in a post I did a while ago on Sam and Dean as living dolls--basically paralysis often with muteness and initial mental incapacity:
http://spnstoryfinders.livejournal.com/8853565.html#comments (http://spnstoryfinders.livejournal.com/8853565.html#comments)
I'm always looking for more recs on this fascinating doll-like state...