No course gets more than one hole in these!
Thomas did not specify that in his original post, and the title does not either.
No, he didn't, but it's a lot more interesting that way, than picking three from Crystal Downs and four from Cypress Point and three from Royal Melbourne, as a true "best 18" would likely produce. And the Good Doctor surely built enough great courses to provide worthy candidates for all the holes.
I'm traveling today, so I don't have much time to think online, but here would be some of the candidate holes [all par-4's unless otherwise noted:
The Jockey Club (Red): 10 (5), 16, 18
The Valley Club: 3, 4 (3), 5, 11 (3), 14 (3), 15 (5)
The Meadow Club: need help here, it's been ages: 7th ?
Cypress Point: 9, 15 (3), 16 (3), 17
Pasatiempo: 1, 5 (3), 10, 14, 15 (3), 16
Claremont: 11, though that hole might pre-date MacKenzie
Crystal Downs: 1, 5, 6, 7, 8 (5)
U of M: need help
Ohio State: need help - if there is anything left
Augusta: 5, 8 (5), 12 (3), 13 (5)
Palmetto: 2, 7 (3), 10 (5), 14 (5)
Royal Melbourne West: 3, 4, 5 (3), 6, 10, 11, 17
Victoria: 9 (5), 15
Kingston Heath: 15 (3) was really his only hole
Royal Adelaide: 3, 4, 11, 14
New South Wales: 5 (5), 7, 14
Lahinch: 9, 10, 11 (3), 13
I will let our UK contingent nominate some holes there. 10 at Cavendish has got to be in the list. 8 at Moortown is not as good as 8 at Crystal Downs, but the Doctor was fonder of the former, having never seen the latter finished; and Crystal Downs has plenty of other candidates.
Note: funny that I haven't picked many 18th holes at all. Ran used to say these were my weakness ... maybe I was just imitating without thinking about it.