Walking shoes. A pair of comfortable walking shoes is your must-pack item. This is a walking town, with notoriously steep and uneven streets, and if you fail to pack for it, your feet will pay. If you are planning an outdoorsy day or side trip from the city, you will need a pair of hiking boots or shoes with good treads.
A good raincoat. San Francisco is in California, but it doesn't adhere to your idea of California weather. It does stay mild year-round, but this is a peninsula surrounded by water on three sides, so you will want to plan for foggy mornings,
Sweaters. San Francisco weather can be a bit unpredictable. One minute you could be comfortable, and the next, shivering with the cold. Having a sweatshirt or sweater with you at all times will alleviate this.
Scarf. Lightweight and easy layers offset those sudden chills. In spring or from September to November, you can bring a lightweight one, but you will want warmer options for the rest of the year.
Backpack. A lightweight daypack is handy for toting those layers, along with sunscreen, a hat (the sun does often come out), and a change of shoes if you are planning a variety of activities, say, hiking, sightseeing, and then drinks.
Wine-bottle protectors. If your visit to San Francisco allows time to visit Napa and Sonoma's amazing vineyards, you may well want to bring a few bottles of wine home with you. Protect those precious liquid souvenirs (and everything in your suitcase) with bubble-wrap wine-bottle protectors.