I would hazard to guess that Rick(Galaga) has made more than just a few trips to SF.
SF on a honeymoon is all about the touristy stuff. Another nice, romantic thing is the Blue and Gold Fleet's cruise around the bay. They also have a dinner cruise that should be nice that time of year. Also, Muir Woods is only about 30 minutes across the Golden Gate Bridge. One of the true natural spectacles.
If you are adventurous the Castro is a great place to people watch. But I would avoid the Haight as the panhandlers are quite aggressive.