2223 has a nice private room at the back and still remains my favourite SF restaurant overall (although of course there are places with better food if that is the key criteria).
Eureka Lounge can also set up a private room at the back and have decent food and a good corkage policy if you wnat to bring fancy wines along.
Farallon is very camp and also has a nice private room if you want something more flash and of course the other big names above are all very good too.
As everyone says, it is hard not to be somewhere gay friendly in SF although it does happen on occasion!