Good question and my answers have changed over the years! I can't pin point just one favourite course but the following are very special:
overall best experience: Ville d'Este near Como, Italy superb par threes, the one course my wife felt comfortable wearing pearls while she played. I played well in the Italian Open and returned 30 years later, it was still wonderful.
Rest of Europe: Royal County Down, Dornoch, Elie and the Old Course (on Thursdays) All great fun to play, sad to finish 18, never a dull moment. Carnoustie is the course to play when looking for your game.
Canada: private, St. George's in Toronto, great test of golf with only a few annoying "improvements". Have not played this century though. Capilano in BC is close second. The National in Toronto in the 1980s.
Resort Courses: Banff, Jasper and the Highlands leave you happy to be a golfer and able to play them. Lucayan CC in the Bahamas and Cinamon Hill in Jamaica are also outstanding golfing experiences.
US: Congressional, Maidstone, Cypress were very memorable and pretty hard to beat.
so many courses and so little time left...