Tim Bayliss (Homicide) for sure needs to be nominated for this one. I mean, canon put him through enough already, but some of the stuff that fanfic put him through (including, I'll admit, yours truly)....

ETA: The fandom is very new, but I'd say Ben Sherman (Southland) has already been put through the wringer in more than one story and probably qualifies as a woobie as well.

(no, I don't have a type at all, do I? ;-))