In compiling a list of injuries, I went for the stuff that caused the most physical anguish for the elder Winchester. This list doesn't look at curses, illnesses, hallucinations, etc. This is just the plain physical injuries, and the agony that comes with them (yes, it's kind of sick how we hang on those).
Here are the more memorable injuries for Dean, in no particular order.
Dean: Look, Sammy, what can I say, man, it's a dangerous gig. I drew the short straw. That's it, end of story.
Sam: Don't talk like that, alright? We still have options.
Dean: What options? Yeah, burial or cremation.
Shot in the shoulder while a sitting duck in a jail cell - "Jus in Bello"
Good thing Nancy the jail secretary was there to patch the wound, because Sam's nursing skills suck.
This one still makes me bust out in tears every time I see it. Wibble....
Cerebral edema from car crash - "In My Time of Dying"
The hottest looking disembodied spirit on the planet.
Beaten beyond recognition by Samifer - "Swan Song"
One of the scariest times ever on "Supernatural." I just kept screaming, "You're destroying the pretty! NOOOOOOO!!!!" Thank Chuck for healing angels.
Beaten beyond recognition by Castiel - "Goodbye Stranger"
Hmm, this scene seems strangely familiar...
Beaten and choked into a coma by Alastair - "On The Head of A Pin"
If only Sam had arrived ten minutes earlier. But then, we wouldn't have gotten this!
Beaten unconscious by the nerd angel - "Point of No Return"
Great job Dean. Provoke that all powerful being that's a little pissed at you right now.
Shot, left for dead in the water, and later has Sam's thumb pressed into the wound for more agony while being beaten - "Born Under A Bad Sign"
That just wasn't Dean's day, was it?
Beaten and nearly choked to death by Sam - "When The Levee Breaks"
This could just be me, but do you think Dean has an issue with people wanting to beat the crap out of him all the time? He sure takes a lot of vicious beatings.
Broken leg ("Hello Cruel World," "The Girl Next Door")
Yes, this one defies all medical logic when he cuts off his cast three weeks after suffering a compound fracture without the help of a healing angel and doesn't even show a limp or any kind of pain. But it was fun to watch before that. (*cough* hospital gown *cough*)
Shot in the back by an angry soap opera husband - "Changing Channels"
That was a very hard way of finding out the pretend soap world caused real injuries. Good thing Sam could fake his way through performing surgery. Yes, that is as weird as it sounds.
Dislocated Shoulder - "I Know What You Did Last Summer"
On the count of three. One...CRACK!
Shot to death - "Dark Side of The Moon"
I said it about Sam, I'll say it about Dean. The prettiest corpse on the planet.
Smacked around by supermodels - "Tall Tales"
Fine, this was more like a dream come true.
Tossed like a rag doll several feet into a car window by a Golem
"Oww, my spleen."
Knocked out and almost eaten by a Rugaru - "Metamorphosis"
Sorry, but this one was just plain gross, especially when Jack helped himself to the growing puddle of Dean's blood.
Finally, I'd be VERY remiss if I didn't go through all of Dean's spectacular "Mystery Spot" deaths
Death by shooting
Death by being hit by car
Death by falling desk
Death by choking
Death by shower mishap
Death by taco
Death by electrocution
Death by accidental axing from brother
Death by mauling from a cute yet highly agitated golden retriever
Death by homicide (which stuck because it was Wednesday)
I know Sammy, I cried too
That's all I have! Any Dean injuries you're particularly fond of?