I haven't visited SF much lately, so I'm not very up-to-date.  But here are some ideas:

Shimo (Outer Richmond district).  It's often said to be the best sushi in the city.  There's also Shimo II in Parkside, an even less traveled neighborhood.

Sebo (Hayes Valley).  It's fairly expensive, though.

Murasaki (Inner Richmond district).

Ino Sushi (Japantown / Pacific Heights, inside the Japan Center / Miyako Mall, possibly unmarked by a sign).  I've heard the service compared to the Soup Nazi, but I always had good meals there.  The sushi is more traditional than at most places in SF, which may or may not appeal to you.  It's tiny, so reservations might be needed.

Kiss Seafood (Japantown / Pacific Heights).  Similar to Ino Sushi: small, with sushi prepared in a Japanese style.

N.B. In case you're interested in other kinds of Japanese food, there are plenty of other good places in Pacific Heights near the last two, including an okonomiyaki joint, some izakayas, manju/mochi shops open during the day, restaurants like Kappa, and so forth.

Three other places that I like, but that aren't necessarily amazing: Grandeho's Kamekyo (in Cole Valley; but it has changed owners, so who knows?), Tokyo Go-Go (in the Mission District; it's trendy and usually loud), Ebisu (in the Inner Richmond district).  All of these tend toward non-traditional sushi (American-style rolls, sauces, etc.).

Hope this helps!