Max Zorin , all he wanted to do was to end Microsoft , is that such a bad thing
Seriously , id say Klove in Scars of Dracula : hes obviously in love with Sarah the blonde girl but he cannot have her due to class differences so even though hes a bad guy you feel a bit sorry for him
People making excuses for Joker , its like a pedo justifying molestation just cuz that person was molested themselves so they get revenge by doing the same. I can agree with Mr Freeze , Penguin or Manbat , those are more sympathetic than Joker imo. But obviously Manbat cant be flying around attacking people 
007 AVTAK : SF mayor was prolly in Zorins pocket so he knew people were gonna be killed and most likely knew his mad Silicon Valley scheme and massive amounts of explosives being driven into the Main Strike mine , same with May Days buddies Flex and Pan Ho.....they couldve pulled out after Bonds chaffeur was killed , so no , they werent innocent but aiding and abetting re : city hall fire , at least thats how i see it.