Depends on what you like, of course. I like the water and find much of San Francisco resembles an eastern city magically transported to California.
I'd say:
1. Get up very early. Take BART to Powell & Market. Walk up Powell a couple of blocks to Union Square. Unless you want to spend all day shopping, take a look around and walk back the way you came. Queue up for cable car. Most go to Hyde Street on the southern edge of the Wharf. Others go to Bay and Taylor, about two blocks south of the Wharf.
The Wharf gets a lot of grief for being an over-commercial strip filled with tee-shirt shops and beer-bellied tourists. And, it is all that. But, it also sits on the bay with great views.
If you are into walking, walk south along the Wharf, then along Fort Mason, by or through the Marina District along Crissy Field to the vicinity of the Golden Gate. You can walk all the way to the bridge, if you like and your feet don't complain. It's a long walk, so wave down a cab to return.
Across the bay, Sausalito and Tiburon are worth a visit. You can take a ferry from the Wharf or, during the work week, from the Ferry Building down the Embarcadero. Since you'll be there in January and the sun will set around 5pm, consider going over to grab dinner. Both towns are tourist meccas, but Tiburon is likely to have fewer folks crawling about. Be sure to take note of the time the last ferry leaves for the city.
If you are a cycler, rent a bike and ride over the Golden Gate, drop down into Sausalito, rest, eat, and come back on the ferry. (Bike rentals are available along the Wharf close to the ferry dock. I'm not sure about the Ferry Building.) It's about a 16-mile trip one way.
That's my opinion. Check the travel sites for their recommended one day SF itineraries. It's a great place.