Swan Oyster Depot is fantastic and affordable. It's a San Francisco institution. Get there early to line up at the counter for a breakfast of oysters, shrimp cocktail and chowder.

The locals favorite is Swan Oyster Depot - it's a small place so you'll have to be patient (or grab a snack before), but well worth the wait. Enjoy!

Scoma's Restaurant  up at the piers, but not quite in the heart of the touristy area, so it's not as gut-wrenchingly overpriced. Really good food, and huge portions.

Anchor Oyster Bar in the Castro is also great, especially if you're looking for shellfish. 

If you want to go to a real original San Francisco seafood place, and you're up for a little adventure, then you have to try Swan Oyster Depot on Polk Street. It's only open for lunch, accepts cash only, you'll need to wait in line, but it's so worth it!  But only go if you're into crab louie, oysters, clam chowder and that kind of stuff.  Seating is along one long bar but the staff are so entertaining and the seafood is super fresh.  It's not cheap, but it's also not expensive and what you get from food quality to experience is worth it.

Another place that's old school SF with great booths and specializing in seafood is Sam's Grill on the corner of Belden Lane.  

Take a short drive south to Half Moon Bay and visit Sam's Chowder House http://www.samschowderhouse.com

"Seafood" is a bit too vague..especially in SF.  Here goes my best stab:

Sushi:  Sanraku on Sutter.  Not the best Sushi, but I think the best sushi for the value.

Crab:   Thanh Long (4104 Judah St).  Garlic Crab and Garlic noodles, Vietnamese style (not cheap, but an SF favorite).

Oysters:  Waterbar has an oyster happy hour 11:30am to 5:30pm, $1 oysters.

Clam Chowder:   Pier Market Seafood Restaurant inside Pier 39.  SKIP THE OUTSIDE STREET VENDORS. Go all the way inside Pier 39, near the carousel.

Sometimes  Primo Patio Cafe (214 Townsend St, near AT&T Park, only open for lunch) have a crispy grilled trout (under $10)

I agree with  Swan Oyster Depot mentioned above.  But, man, the line is long.  

Tadich Grill in the Financial District is old school SF and fantastic but it's pricey.

Woodhouse Fish Company in the Castro and Pac Heights is good as well but it's starting to remind me of a chain restaurant.  

Fish tacos at  Nick's Crispy Tacos,  Tacko, or  The Taco Shop at Underdogs in the sunset are the best fish tacos in SF.  

Hope this helps! 

Chris  

Anchor Oyster Bar in the Castro

You should try The Waterfront Restaurant. I would not call it cheap, but it's cheaper than what you find in Pier 39. If you go there, make sure to ask for a place on the terrace. It has a great view of the bay and it's surrounded by tall glass panels so wind is never an issue.

I like Mission Rock Resort because you can get an amazing view of the bay, and it's out of the way enough to not be super busy. 

For sushi I like Live Sushi Bar , and Sushi Time . 

I like  Crustacean.  Also, if you have a car, and would enjoy a beautiful drive then try  Nick's Cove & Cottages  thats great for an afternoon lunch or early sunset dinner. 

You might try  Anchor & Hope

Bar Crudo is one of my favorites. They have a great happy hour! The chowder is legendary (but not your typical new england style with the addition of chorizo). My favorite is the arctic char crudo, and oysters of course.

I would recommend restaurants in the Little Italy neighborhood located at the North Beach. Near the  Washington Square Park. Enjoy!!

Swan Oyster Depot : 1517 Polk St. I love that place so much ! You eat at the counter. This place must have almost 100years old ! It is not expensive. Beware : you have to go very early or it will be packed. From 8:00 to 5:30 monday to saturday . Bon appétit !

Swan Oyster Depot 1517 Polk Street, San Francisco

Scoma's Restaurant

Woodhouse Fish Company is likely the best bang for your buck.  Swan Oyster Depot is fantastic & tasty however you'll need to wait in line, pay a handful and its CASH ONLY.

Pesce Seafood Bar in the Castro is really good. Venetian-inspired tapas 2223 Market St, San Francisco.

Swan Oyster Depot is a wonderful experience.  It's small, counter seating only, and you will most likely wait to get seated, but it's worth it.

I haven't been to this one but heard it's good - The Old Clam House - 299 Bayshore Blvd.  Harrison to Bayshore or 101 to Bayshore.

Sotto Mare in North Beach!! Best ciopinno in the city. Cash only, like all the good spots in north beach. 

Sotto Mare in north beach is good!

Go to Fisherman's Wharf, it in the street carts outside the restaurants, it will be a few bucks cheaper.

I'm not a seafood fan but have heard good things about Pacific Cafe in the Richmond District.

If you are into peruvian food Fresca in Fillmore is an amazing restaurant with plenty of ceviche options that are a complete delight.

Also there is La Mar in Pier 1.5 that could be a little up in the price range but very recommended. 

If you have a chance to get to the Alamo Square neighborhood, I would recommend the Alamo Square Seafood Grill on Fillmore Street. It's just a few blocks from the painted ladies.

Sushi Zone at Market & Pearl is some of the best value you'll find. Here's their Yelp page: http://www.yelp.com/biz/sushi-zone-san-francisco

Arrive before they open if you don't want to wait for an hour. They don't take reservations over the phone, and the place is small.

Pacific Cafe: Small...great atmosphere and great seafood. Tadich Grill downtown is great too for a restaurant that's been around a long time.  

You see, after a few people answer, you are left with more choices than you have time. Traveling is about self discovery. Go find your own restaurant that hasn't been suggested. If you can do that then you will become the one with the answer.