Okay, just a few off the top of my head:
Fool Moon - beaten badly by the Lycanthropes, overused his magic to the point of not being able to use it for awhile, watched Carmichael and a bunch of other SI cops die horribly
Grave Peril - Besides Susan getting turned whatever the vampires did to him in the dark that he still has nightmares about, poisoned himself with toadstool, bad head injury, got a bunch of his magic taken away by the nightmare, died for long enough to leave a ghost to help him beat up the nightmare.
Summer Knight - Saw the queens with his sight, stabbed himself in the hand with a letter opener, found out Elaine was alive
Death Masks - tortured by nicodemus, Saw susan again and she told him it was over for good, Saw shiro die horribly
Blood Rites - Can't think of any besides what you mentioned
Dead Beat - Tortured and almost killed by Cassius, Leg injured and almost killed by corpsetaker
Proven Guilty - Watched the kid at the beginning get killed
White Night - Got fairly beaten up in the duel with Vito Malvora and the Raith guy
Small Favor - Failed to save Ivy from the Denarians, almost drowned in the fight at the Shedd, had his eyes frozen by Mab, Got his nose broken by the Gruffs, watched Michael get shot and almost killed
Turn Coat - Saw the Naagloshi with his sight, saw the Naagloshi kill Kirby and badly wound Andi, Found out that Luccio had been forced into a relationship with him and didn't want to date him anymore
Changes - Car got destroyed, house got burned down, broke his spine, Found out he had a daughter that Susan had hidden for him for years, Agreed to be the winter knight, fought in a magical war at Chichen Itza, killed Susan, got shot and nearly killed at the end.
Ghost Story - Found out he was dead (or thought so at the time), nearly got eaten by wraiths a couple times, Lost almost all of himself by using too much magic, hurt by seeing what had happened to all of his friends since he had "died".