Two days in San Jose
 

I am going to Palo Alto for a wedding. I will have a rental car. I have two full days and one half day that I can dedicate to touring. What do you recommend? I will have a rental car.

Head to The City.

I've been to San Francisco. I'm more interested in Half Moon Bay, Sonoma, Napa, Santa Cruz. I just don't know where to go.

What kind of activities do you enjoy?

See my post under your "two days in Palo Alto" heading.
San Fran- is a good bet. There's also the new Giants stadium which is very nice on/by the Embarcadero. (I'm not a Barry Bonds fan but i do like the new stadium). That area is being built up and there are lots of clubs/eating places. You can rent bicycles next door and cycle the Embarcadero (its flat).
Santa Cruz/Capitola/Seascapes-take a walk on ridge by the Surfing museum in santa cruz. Stroll downtown santa cruz (warning!some of the people you will see are eclectic)-go to the hat store and the Annie Glass store, just to mention 2, but there are more interesting shops. Go to the beach/shopping at Capitola, not my favorite but a lot of people like it. I like Seascapes resort for lunch and then a walk/day on the beach there. Rent bicycles @ the hotel and ride around the area. Or maybe stop @ Gayles for sandwiches. Further up the coast near the Ritz Hotel is pretty but the whether can be overcast.

If those were my two days, I'd head out to Monterey/Carmel after the wedding and spend the first night there. You could go to Monterey Aquarium or walk along Carmel Beach or wander around Carmel, maybe even go to Point Lobos.

Next day, I'd drive leisurely up the coast, maybe lunch in Santa Cruz or Half Moon Bay and keep going on Highway 1 into San Francisco, over the Golden Gate Bridge on Highway 101 and end up in Sonoma County. Go wine tasting in Sonoma County and Napa the rest of the time left and then fly home.

Of course, if you like hiking, you could substitute hiking for wine-tasting.