I'm out of area as I write this but after giving it some study here goes a listing of my personal 50 best.
I have not played Augusta or Chicago so I mention that right up front and therefore cannot include them. Ditto all the comments people have posted regarding Friar's Head.
Let me also mention that I've left a few spaces blank (4 in total) from my personal top 50 since there's always some "new" course that may challenge for a spot. Here goes ...
Top Ten (in no personal order)
Shinnecock Hills (the best course in the USA IMHO)
Oakmont
Cypress Point
Pine Valley
Pinehurst #2
The Golf Club (Pete's best I've played including Teeth of Dog)
Merion / East
Winged Foot / West (the most intense second shot course)
NGLA (if you love "pure" architecture one needs to see it)
Sand Hills (a surreal experience)
2nd Ten
Plainfield (deserves no less a placement)
Pebble Beach
Prairie Dunes
Camargo (the best Raynor I've played thus far)
Seminole
Pacific Dunes
Pete Dye
Wannamoisett (the best middleweight course I've played)
3rd Ten
SFGC
Bethpage / Black
Crystal Downs
TPC Stadium
Bandon Dunes
Riviera
Olde Kinderhook (the best Rees course I've played and is vastly underrated because of its location in Albany NY)
The Kingsley Club (after giving it some thought I can't say anything less about the course -- superb fun indeed!)
Muirfield Village
TCC
4th Ten
The Ocean Course (the Darth Vader of sheer intensity!)
Fisher's Island
Karsten Creek (very underrated TF design -- just watch the NCAA's this week)
Ocean Hammock (dynamite layout by Jack -- how it doesn't get rated above so much in FL by GD, GW, and GM is beyond me!)
Arcadia Bluffs
Olympic / Lake
Whistling Straits
Black Mesa (people need to see this wonderful Baxter Spann design just outside of Santa Fe)
Inverness
5th Ten
Valley Club of Montecito (how GD dropped this course from the top 100 is indeed puzzling -- Mackenzie gold!) When others mention the qualities of Somerset Hills I'd point them in the direction of Santa Barbara to see how such a short course can be so compelling.
Milwaukee (the one course often overlooked from Wisconsin)
Whisper Rock (the "new" Desert Forest)
Chapparal Pines (replaces Forest Highlands Canyon Course as best in the ponderosa area / Gary Panks did a first rate effort and the course loses out to the "eye candy" approach you find at the neighboring The Rim).
Hollywood / NJ (how the course doesn't get listed among the top magazines escapes me).
Skokie (superb restoration by R.Prichard -- how it goes so underappreciated escapes me. In many ways it's the
Plainfield of the Chicago area.
Wolf Creek / Mesquite NV (like it better than Shadow Creek and it offers more thrills and fun than most can imagine even with a hole or two that borders on insanity!). Shadow is a wonderful testament to the ability of man to conquer the terrain -- I just see Wolf Creek being such a wild and exciting adventure although I admit it won't be everyone else's cup of tea).
Chirichua (Desert Mountain) replaces Desert Highlands as the best Nicklaus course in the Scottsdale area and highlights the "new" Nicklaus approach. Makes you play all the shots and doesn't overdose on difficulty as the Geronimo. Jack did a first rate effort with a superb short par-4 in the 2nd hole, to name just one example -- ditto the back-to-back par-4's 9th and 10th.
Olympia Fields / North (liked the course prior to all the Open changes. Have not played it since all the existing work was completed but the greens and bunker work when I was there was indeed first rate stuff.
On my last note you'll see a few of Pete Dye courses sprinkled throughout my listing. I've said this before but I see him as the finest architect in the last half of the 20th century and wanted to include a number of his most significant efforts. Others such as Harbour Town and even Oak Tree (ahead of Honors) and the Stadium at PGA West would likely make my top 100 listing.
I also like Pasatiempo and World Woods / Pine Barrens but don't believe they have the stuff to make my top 50 although I would certainly recommend anyone to play them when in the area.
Let the bullets fly ...