One of my wife and my favorite things to do is go to this place in the Inner Richmond called Green Apple Books. We're both bibliophiles, so we'll go there and spend a lot of time.
There's a great dim sum place nearby called Good Luck Dim Sum. Good Luck is the kind of place where two people can spend $15, and you're incredibly full, and then you still have a thing of leftovers. You can pick it up and take it to the park and eat it there. If you're not into dim sum, there's a place called Bunn Mi that I think is the best banh mi in the city.
One of our other favorite places is a place in the Mission called Wise Sons Deli. You can't go wrong with the Reuben there. They make their own pastrami, and it's the best I've ever had.
If we're in the Mission, we'd walk up and down Mission and Valencia, and just window shop. On Valencia, you can't go wrong with Ritual. That's quality coffee. Borderlands Books is an amazing place for sci-fi, fantasy type books. Paxton Gate has great quirky nature stuff and jewelry. It's really interesting and a fun place to browse. They have some weird taxidermy.
Right next to Paxton Gate, there's a pirate store. I think the deal is they wanted to open a tutoring center and couldn't get it zoned, so they opened up a pirate store. There's tutoring in the back.