We did a driving tour of Cali 2 years ago and San Francisco was by far the best part. I absolutely fell in love with this city. Where we stayed it was called the Lombard Motor Inn. I was OK, not bad not super. What was great about it was the location, it was just a few blocks from trolly and we took that around and walked quite a bit.
There is quite a few restaurants around there and more on the trolly routes.
I believe that the subway went to AT&T park, I think that I saw it on the maps posted around but I cannot say for sure.
I wish I could have stayed there longer and explored more and in turn give you better answers but if you go like I said this is my now favorite city and I cannot wait to go back.
EDIT
Also I was watching Worlds Weirdest Restaurants on Food Network earlier and they went to the Tonga Room and it looked great and very fun.
http://tongaroom.com/