3 Days in SF--need recs
These are all great - look up the respective menus online. I believe all can also be booked via OpenTable.com
Pres a vi - new hotspot, small plates & great wine
Perbacco - also new and yummy
Slanted Door - awesome location, awesome food(tough to get res)
Garabaldi's on Presidio - consistently great, neighbor feel
Frascati - see above
I would highly recommend spending 15-20 minutes scrolling thru the prior posts already on this board. You will find the question you are asking appears here at least once or twice a week. There are many, many helpful suggestions, comments and recommendations already here and available to you.
Your query is so vague you won't get anything more than you'd get just reading posts. This question is asked at least once a week and it's impossible to help you out if you dont have any specifics (price range, neighborhood, ambiance, where you're staying, where you're coming from, preferred cuisines, etc etc).
For instance: http://www.chowhound.com/topics/360116
Indeed, there's so much to choose from and trolling through the board will be helpful. My best buddy from NJ did the stayover before her honeymoon in HI (20 years ago), and still talks about that ferry ride they took to Sausalito and their lunch at Scoma's. Don't know anything about it today, but sounds like a romantic option for 2 honeymooners with a few days in SF.
I've been to Poggio a few times and have just not been impressed with the food. Haven't tried Fish, but it is spoken highly of here. If you don't want to leave SF I'll toss out some names - Aziza, Isa, Luella, Tadich, Zuni. Isa and Luella are neighborhood places - Tadich and Zuni are SF institutions and Aziza is interesting and something you're not likely to find anywhere else. Enjoy your brief stay!