Fireworks are great!  We watched from our balcony at our room at the Hotel Vitale last year.  It's right near Ferry Building, anywhere along there is a great place to see fireworks over the Bay.

American Cupcake [CLOSED] does a beer/wine and cupcake pairing! It was an interesting and fun thing to do for us.  Although we did get wasted with a sugar high at 1:00pm... One of my favorite places to eat in San Fran is the Cliff House, the food is moderately priced but the view and ambiance of the building always puts me in awe; especially looking down at the sutro baths.

Try the Inner Richmond. You can't go wrong with a sandwich from Cafe Bunn Mi, Lou's Sandwiches Cafe, or Arguello Super Market if you're heading to Golden Gate Park. If you're looking to sit down then Shanghai Dumpling King has the best soup dumplings in the city, or check out Amphawa Thai Noodle House for excellent thai cuisine. If the weather is any good then Baker Beach has some fine views of the Golden Gate Bridge. And if you need some reading material, Green Apple Books is one of the best independent bookstores around. 

I'm pretty good with food in SF! :)  San Franciscans seem to love waiting in line for food, so be prepared for that at most of the places I'm going to recommend, but if you show up at opening, you should be good.

For inexpensive ethnic...

• Lately, I've been dreaming of San Tung Chinese Restaurant fried chicken.  Very down home Chinese restaurant, but people have caught wind of how amazing their fried chicken is, so there's always a line
• Two other places where there's always a line as well: Katana Ya and Ramen Underground, both for ramen
• El Farolito is my favorite for Mexican.  Their quesadilla suiza is the best and splittable between two people if you get an appetizer, like a plate of nachos, or a couple tacos
  

Oysters:

• Waterbar right on the water on the Embarcadero is a super gorgeous restaurant with an oyster happy hour 7 days a week (I believe from 11 AM-5 PM).  Dollar oysters with a gorgeous view!  On weekends, they also have a drinks happy hour in the middle of the day.
• Farallon is another really nice restaurant that has a fab happy hour, which I believe runs from 4:30-6 from Tuesday through Saturday in their Jellyfish Lounge, and they have dollar oysters on the menu.  They're in the heart of downtown.
• For chowder, specifically, hit up the more touristy part of the Embarcadero from Pier 39 to Fisherman's Wharf. A fun place to stop by there is the Boudin Bakery & Cafe.  They've got chewer and a cool gift shop!

Pizza:

• Tony’s Pizza Napoletana is very popular.  They serve authentic  Italian wood fired pizza
  
• Pizzeria Delfina and Zero Zero are also pretty amazing for the thinner, flakier crust pizza
  
• If you like deep dish, Little Star Pizza or one of the Patxi's Chicago Pizza is where you want to be

Sandwiches:

• I LOVE Bite in the Tenderloin.  I used to live close to there and that specific area is not for the faint of heart and not somewhere I'd go for dinner, but lunch is fine.  They have some pretty amazing sandwiches, like The Kitchen Sink, which is full of meat and like, seven cheeses
• Ike's Place is very popular.  There's going to be a long, LONG line here.  Even if you order online and go there, you still have to wait in line with all the other people who waited online.  If you do want to try a sandwich here from their awesomely extensive menu, be sure to order online
  

I've been to see Beach Blanket Babylon before, and if you're into catch a live musical, it can be fun!  What I love is that they're constantly updating the show.  Unless you catch a show a few days apart, it's never the same show.  They're always updating their songs with current events.  You might be able to find discounted tickets on Goldstar.

I have not caught New Years Eve fireworks anywhere in a while, but the most popular spots are along the Embarcadero or at Union Square.  There will likely be a lot of people there.  Other nature-y spots, like the top of hills (Bernal Heights, Grand View Park) and beaches (Ocean Beach, Baker Beach, Lands End) come to mind, but there's likely a curfew for those spots (wouldn't stop a few people from hitting them up, though!).

Hope you two have a blast! :)

Hey Scott, I actually wrote several blog posts about fun non-touristy things to do in San Francisco. Each one focuses on a different section of the city, and includes lots of great food and fun activities.

The Mission and the Castro

Mission street art and dessert

Chinatown, North Beach, and the Embarcadero

Golden Gate Park and Ocean Beach

Golden Gate Bridge, Sausalito, and Fisherman’s Wharf

Oakland:

First Fridays, Art Murmur, and a burlesque show

Here are some inexpensive food recommendations:

• Yamo for hole in the wall Asian noodles
  
• Deja Vu Pizza & Pasta for great calzones
  
• Dumpling Kitchen for amazing soup dumplings
  
• SoMa StrEat Food Park for food trucks
  
• Truck Stop for food trucks in downtown
  
• Off the Grid: San Francisco for food trucks on Fri night
  
• Arinell Pizza Inc for New York style pizza
  
• Kasa Indian Eatery for kati rolls
  
• Hong Kong Lounge for dim sum
  
• New Eritrea Restaurant & Bar for Ethiopian
  
• Playground for Korean fried chicken
  
• SB40 for Filipino food
  
• Humphry Slocombe for ice cream
  
• Ramen Underground for ramen
  
• Muracci's Japanese Curry & Grill for Japanese curry
  
• Ike's Place for sandwiches
  

That's just what I came up with off the top of my head. There are too many places to name. 

Let me know if you have any other questions!

We travel to SF about 10 times a year and love it! It's great to dig deeper in to a city and as foodies I am thrilled you wrote this question. I am saving every answer! I have discovered Chris Milano's Foodie Adventures - a walking food tour in the city. I have been on the Mission District tour as well as the North Beach -San Francisco Chinatown tour - they are phenominal and the food is crazy good http://foodieadventures.com/FoodieAdventures/Chris_Milanos_FOODIE_ADVENTURES%21____San_Francisco_Food_Tours____Culinary_Walking_Tours_of_San_Francisco____Tour_Info.html

This is the link to the site. If you want more details I have written posts on my blog! If you have questions let me know. Everyone else has given you many great tips. Enjoy!

My wife & I went to BBB 20-25 years ago. It's longevity is testimony to its allure. We enjoyed it immensely.

Insofar as off-the-touristy beat, we love good ole Perry's on Union Street both to meet locals and have a great not-too-pricey meal.

Food Truck Heaven is Roli Roti's porchetta sandwich, available at the Ferry Plaza Farmers Market on Thursdays 10:30 am to 2:00 pm and on Saturdays 8:00 am to 2:00 pm. http://www.roliroti.com/porchetta 

Very good, inexpensive Vietnamese food at Tin Vietnamese Cuisine in SOMA.

Have you walked along Lands End - the coast west of the GG Bridge? http://www.nps.gov/goga/planyourvisit/landsend.htm There is a labyrinth to walk http://www.weekendsherpa.com/stories/hike-lands-end-labyrinth-san-francisco/ Also, there are tree lined trails in the Presidio. 

- Outdoors: check out Sutro Baths, Lands End, Ocean Beach, Crissy Field, Golden Gate Park, and Lyon Street Steps. Great if you want to walk around and see good views. 

Cheap Eats:

- Take out dim sum at Wing Lee Bakery or Good Luck Dim Sum on Clement St. Wait in line, order at the counter, and point at what you want. Buns at 95 cents and you get 3 dumplings for less than a dollar. 

- Mandalay Restaurant for Burmese food. More "mom-and-pop" than the much hyped Burma Superstar. Both are near each other though. 

- In Chinatown, check out Golden Gate Bakery for their famous egg custard tarts. Their opening hours are unpredictable, so call before you go. 

- Balompie Cafe in the Mission for Salvadorean pupusas. So good!