The October 2006 issue of Gourmet has a list and short description of what they consider to be the top 50 restaurants in the US. They also repeat the top 50 restaurant list for 2001. There have been many changes in 5 years.
#1. Alinea in Chicago. Grant Achatz is supposed to be redefining the American restaurant for an entirely new generation. You get many tiny samples of wildly original creations. When he perfects a dish he drops it and replaces it with something entirely new. Thus your meal on a return visit may be wildly different. Matching wine must be a nightmare, considering the extreme difference in the many bite sized courses. One course is a single perfect bite of lamb served in smoldering eucalyptus leaves. A tiny ravioli is filled with very intense liquid truffle. But these dishes likely have been replaced by something new by now.
#2 Chez Panisse in Berkeley. One hardly needs to discuss this long time top restaurant of Alice Waters.
#3 The French Laundry/Per Se. These two Thomas Keller restaurants hardly need any discussion. It is interesting that in the kitchen of each you will find a TV monitor tuned to the kitchen of the other restaurant. I guess this helps Keller keep control of both restaurants despite one being on the West coast and the other on the East coast.
#4 Spago in Beverly Hills. Despite being a restaurant for the stars, this restaurant still manages to put out top food.
#5 Joel Robuchon at the Mansion in Las Vegas. Apparently this new restaurant is turning out top food despite the location. It also is very expensive.
There now are many restaurants on the top 50 list scattered nearly all over the US. Most of these restaurants likely have a decent to outstanding wine list, but I doubt if you find any bargins in most of them.