I am not an expert on San Francisco, but I did just return from my third vacation there, so I thought I would join Trip Advisor and talk about my trip, get ready for future trips.
What to pack: My wife and I packed clothes to layer, which I'm glad we did because the bay city wind factor plus random spurts of sunlight can get confusing. So when you pack, be prepared for a temp which ranges from 40 at night to 60 during the day (or maybe a little warmer-depending on when you go.)
Hotel: The best thing to do is if it's a special or romantic occasion is to splurge, but if you're on a romantic budget trip (a contradiction of terms, i know, but follow me) you might want to just surf the net until something catches your eye. The thing about hotels in San Francisco is that San Francisco hotels cater to diverse groups and their amenities and their presentation reflect this diversity. The best thing to do is research the hotels until you come across something interesting. My wife and I, for example, on our fifteen wedding anniversary we splurged and stayed at Hotel Monaco, but when we came back recently we stayed at the Hotel Union Square which is probably the best deal (four stars and for a lot less). Don't feel anxious about getting a hotel. Bed and breakfast is always an option, but probably best for those who want to relax in a home away from home. You should also call the bed and breakfast and ask about the personality of the place. Red Victorian Bed and Breakfast (www.redvic.com) for example, is far more social an atmopshere. Each room has a different theme. My brother and his wife stayed there and loved it, but he said it's not for who want a quiet place to stay and cuddle up. For that you might want to try Delores Park Inn or some smaller bed and breakfast in the wine country.
Don't drive your car, rent one for a day: Driving in San Fran is a love/hate relationship. You might spend an hour looking for parking in the city. It's true some of the best things to see, it's best to drive to, but it's even better to do a hybrid between public transportation and rental car. Buy a Muni week pass too when you get there (http://www.sfmuni.com)
What to Do: First thing, buy a Go Card (www.gosanfranciscocard.com). This can help out a first timer to the area. I wish my wife and I had it the first time we went to San Fran. We had it during our last visit and enjoyed ourselves. Basically it's a card you buy and it covers most (if not all) of your admissions to San Fran area attractions. It also takes the burden of money off your shoulders and is also unlimited. Once you pay for the card, I had to pay for little else. Mostly bought things for the kids, dinners etc. For a list of admissions go to (gosanfranciscocard.com/freeadmissions.html)
Then just explore. Walk as much as you can and when you're at Fisherman's Wharf walk to Hyde Street Pier. There are a lot of old ships you can look at. Also, make sure you walk at least once across the Golden Gate Bridge. Visit Alcatraz. Visit SFMOMA at some point and the Japanese Tea Garden, Go to Twin Peaks at night. Go to Fort Point (you might recognize something from the movie Vertigo there)
Dinner: Make reservations for dinners in advance (if you can). Try new things while you are there, there is something for everyone. I would recommend asking your hotel conceirge while you are there where great places for lunch/dinner are (do a little research before hand) because that's what they are there for. Also, it's good to just try new things some favorites that i have enjoyed are (Acme Chop House, PJ's Oyster Bed, John's Grill, Harpoon Louie's, and for Sunda brunch I suggest California Cafe, Shanghai 1930, ) Whatever your flavor, there is something for you.
Hope this helps you all out!