It depends what you care about.
Quince has a beautiful space. Service is casual but well-oiled and highly competent. The atmosphere is semiformal - conversations are conducted at a loud murmur. Food is tasty and portion sizes are perfect - but the food doesn't hit the highs (or potential lows) of a more creative menu. I really enjoyed my experience here.
Atelier Crenn has a very casual room and pretty casual service considering the price point. I would characterize the service as well-meaning and eager to please but it's not a smoothly oiled operation. The food portions are small. The food is wildly creative and beautifully plated. I still remember many of the dishes I had in my two visits there - but the experiences were not smooth ones (some of the dishes were misses, service mistakes, only one bathroom etc.).
Gary Danko is a formal restaurant of 20 yrs ago. Think of a place that Richard Gere would take Julia Roberts in Pretty Woman. It offers the formal experience and food standards that many crave.
If someone else were paying, Crenn and Quince, since I'm probably never going to either on my own dime.
Gary Danko's menu seems stuck in the 90s and it's pretty much the opposite of an only-in-SF experience, neither of which are intrinsically bad things. They don't have an endurance tasting menu like the other two, their "tasting menu" is just a choice of five dishes from the a la carte menu.
1. Atelier Creen
3. Anywhere but Gary Danko
4. Anywhere but Gary Danko
5. Anywhere but Gary Danko
6. Anywhere but Gary Danko
7. Anywhere but Gary Danko
8. Anywhere but Gary Danko
9. Anywhere but Gary Danko
10. Anywhere but Gary Danko
11. Anywhere but Gary Danko
12. Anywhere but Gary Danko
Needless to say, there are at least a dozen other restaurants I would rather eat at than Gary Danko. It is very staid and hasn't changed its menu in years.
Depends on who I am dining with.
In terms of service they are all excellent Danko is more stiff and formal. I find Quince and Creen to be professional but more casual and I personally prefer that style.
In terms of creativity it goes Creen, Quince then Gary Danko.
Gary Danko for conservative business clients, Quince for parents and Creen for foodies and friends.