I've been to all four and they are all good, but depending on what you are looking for each has its advantages.
Fleur de Lys is most romantic of them all. It's small, intimate, great service and excellent food. The couple of times that I've been there, I didn't like their tasting menu, I found the a la cart to be more interesting. If you end up there, you HAVE to get the fois gras terrine, it is the BEST fois I've ever tasted it.
The last time we were at Masa's was in June. They redid the interior from last year. It is now much nicer inside, modern, more sense of space (though it's still small) The food was good, but after eating out at this type of restaurants so frequently, our pallets are spoiled. For the amount of money they charged, it was not extraordinary.
I went to Farallon two year ago. I can't remember if the food was great of not but I'm sure it was not too bad. The interior was great, very whimsical and well suited to the seafood they serve there.
Aqua is loud and flashy. Lots of power suites and business people. Their signature dish black mussel soufflé does not disappoint, you have to order that if you go there.
One thing I don't like about all these places is the inability to accommodate the table in their menu choices. It's everybody have to order the tasting menu or nothing. To get the most flexibility and great food and service and everything else you can ask for, try Gary Danko.
re: Wendy Lai
It's been a while since I was there. But I remember I had a shrimp risotto that was to die for. Also I had a duck proschutto (sp?) with honeydew melons that was excellent as well. I doubt the same things will be there. I don't know if Gary Danko has a signature like many other places, perhaps other people can answer you on that