"Against the Clock" by Swanseajill
When Sam goes missing during the investigation of a series of murders, Dean battles illness and the clock to solve the case before Sam's time runs out. Casefic, Sick!Dean
http://www.fanfiction.net/s/4810440/1/Against_the_Clock

"Cliffhanger" by Merisha
When a hunt goes completely wrong, a distraught John has to come to the rescue of his boys. Mulitple POV's. Hurt!Sam/Dean.
http://www.fanfiction.net/s/4542836/1/Cliffhanger

"And the ground shook" by sams1ra
John is faced with his worst nightmare. And now he has to fix everything.
http://www.fanfiction.net/s/3230960/1/And_The_Ground_Shook

And just about every fic by gaelicspirit
http://www.fanfiction.net/u/1128719/

Hope some of these are what you're looking for :)