It really depends on your budget, how many people you plan on being there, the kind of food you want and the atmosphere you are looking for.
If you want very high end, elegant and really, really special (and expensive) I think THE FIFTH FLOOR in the Palomar Hotel can't be beat. I was given a gift certifcate to that restaurant for my 40th birthday and it was the most incredible dining experience of my life. I didn't see the bill, but I'm pretty sure it was well over $300, so it's an incredible luxury.
BOULEVARD near the end of Market and the Embarcadero is another high end and just wonderful restaurant. It's not as expensive as The Fifth Floor, but I believe entrees run in the $40s these days. Good for two people and a romantic evening.
There are many other great high-end restaurants in San Francisco. But if that's not what you are looking for, there are other good choices as well:
CHEVY'S is always fun - Americanized Mexican food, loud, big drinks. Good for a crowd.
LIME in the Castro is also really lively, they serve only "small plates" sort of like Tapas, but not Spanish. A big group of us went there last summer and had a blast. Only thing, the tables are small - but it's fun to crowd together and eat all the little things that come out while drinking fancy drinks.
I could go on and on, but without knowing more about what you're looking for or your budget, it's hard to make recommendations. But here are a few more:
The Fifth Floor: http://www.fifthfloorrestaurant.com/