Ed to answer your question in no particular order:
Augusta, Muirfield Village, Milwaukee CC, Torrey Pines, Sage Valley, Riviera, Troon ( Scotland) Pinehurst #2,#4, Point O' Woods, Pebble Beach, Hazeltine, Merion, Oak Hill, Prairie Dunes, Eugene CC, Harbor Town, Cherry Hills, Scioto, Olympic Club ( non USGA set up) Honors Course, LACC, San Francisco Golf Club, Madison Club, Champions ( houston) Carlton Woods Nicklaus, CC of NC ( cant remember which course is which, did like one more than the other) Kingsbarnes, Cypress Point, Spyglass,
Jack - I totally agree about the weather being a huge factor on the peninsula,, however that is constant over the whole peninsula, taking advantage of particular weather situations on every course is important. However, once again the weather, beauty etc are all part of the experience and not necessarily the design of the golf course. Spanish Bay is pretty, has almost the same weather , yet is one awful golf course IMO.
CPC is ranked as highly as it is , IMO for many factors, the first being that it is probably the most beautiful course in the world, has an incredible history ( the match ) , is very difficult to get onto, ( mystery )
Let me be clear, I don't think that Cypress Point Club is a bad golf course, its very good, but I personally don't think its in the top 10 or maybe 20 in the country. I don't think its the best in its zip code ( pebble ) Mostly because I put zero value on beauty and history when evaluating a golf course. I leave it strictly to the golf.