Whoops, I think I'm late to the party but I can't help but couldn't help bit offer up my 2¢ worth.
I lived in the bay area for a couple of years, more so, the mission district (near Delores Park and the Armoury).
My top picks are these:
Secret Pirate Bar: Smuggaler's Cove in the Filmore.
Bonus: The Sundance/Kubuki Theater is in the Filmore too. Catch a movie there, does not disappoint, ever.
Delores Park and the Murelas: Mission district, Velencia and Guerrero. Beautiful, food filled, lively and just wonderful to pass the day in the park.
Hayes Valley neighborhood. Dinner? Amazing brunch places, Germany restaurant and amazing outdoor metal installation art. A great neighborhood.
Twin Peaks. Get your camera and some hiking shoes. Great 360° views from the peaks, and it's really windy so make sure your hats are snug, if you wear hats.
And last but not least, Hoit Tower. It's a great place to visit. It's the Taj Mahal of SF.