I refrained from adding to this thread until we returned from a family vaca that had us in Napa Valley, San Fran and Central California over 10 days. We lived in Palo Alto and Mountainview for a few years from ~2003-2006 and had spent a fair amount of time in SF.
In short, SF was fine, safe where we ventured and much better than I expected. We stayed at the Mark Hopkins and walked back and forth to Fishermans Wharf, Pier 33, Washington Square and Union Square and never felt unsafe. We did see some folk that had me sticking close to the girls, but I always keep my head on a swivel in cities and this was nothing that we have not experienced in NYC, etc. That said, driving through the lower areas to get to and from the highways was a bit disturbing and sad, but again nothing beyond other major cities.
There were a few empty storefronts on the waterfront, sad to see Aliotos gone, but Pier 39 was mobbed, Alcatraz boats were full, there were tourists everywhere, many European, and the Buena Vista and Scoma's (one of my all-time favorite restaurants) were as great as you expect. We usually avoid the tourist areas, except for Scomas, but this was our daughter's first time to SF so tourists we were.
Funny, back in the hotel I was watching the news and caught some talking head saying that SF was dangerous, a mess and no longer a great city...wonder what SF he was talking about?