The Tenderloin in San Francisco isn't the most savory of spots, but nothing like the places in Southern California. There are some hoods now in Fresno of all places that have become really gang infused.
I can't think of too many others specifically. I'm sure each town has it's section of riff raff and low life, but for the most part from bottom to top or top to bottom, California is just soooo d*mn nice.
You'd be really hard pressed to NOT have a good time in that incredible State.
When are you visiting and how long will you stay?