In Southern California, the Orange County Register, LA Times, Riverside Press-Enterprise and Ventura County Star remain independent of each other. Dean Singleton's company owns the other eight daily newspapers in the area stretching among those four newspapers.
In Northern California, the San Francisco Chronicle and San Francisco Examiner are separate. The Examiner is a free paper owned by Anschutz. I'm not sure as to the Santa Rosa Press-Democrat, maybe someon can help me here. Dean Singleton's company pretty much owns the rest.
I can understand why a reader would really be in an uproar over the NoCal arrangement, since the Chron's owner has engaged in a business deal/transaction with the owner of all the other papers. If I'm not mistaken, there is a legend of a situation where the LA Times people helped front the money for MediaNews' purchase of the LA Daily News.
Business-wise, it is logical to question the level of competition and continued quality of product when two rival companies make deals with each other.