Brandon, interesting question...here are a couple...
16th at Cypress Point – Pretty well documented exchange between MacKenzie and Hollins, but would love to have seen her hit the shot across the ocean and the look on the doctor's face...
Flipping the nines at Augusta – I believe one of the reason's they flipped them was due to the fact that the front nine received more morning sun and therefore they could get earlier start times due to frost, etc. – but it would have been interesting to hear the debate on the merits of each nine's holes/finish from a tournament perspective.
18th at High Pointe – I think the discussions between Tom Doak, ownership, and the DEQ/DNR (not sure if those are the right environmental bodies they had to work with) about the routing of that hole and how it finally came to be.
10th at The Golf Club – The ridge that crosses the fairway short of the green is so unique to me in American course design – I wonder what (if any) discussions Pete Dye had with ownership/membership on including it in the final plan. It is such a small, subtle feature – but so cool and something I have rarely seen here. (EDIT: In re-reading this post and thread, I am now not sure the hole I am thinking of is the 10th...)
17th at TPC Sawgrass – Again, a well-documented hole and how it came to be between Pete and Alice Dye – but certainly would have been interesting to be a part of the first discussion around an island green.
9th at The Kingsley Club – I would guess the most controversial hole at what some considering a polarizing design, it would have been great to been a part of the discussions between Mike DeVries and the team – not only about the green, but the two sets of tees, and subsequently the change in cut lines from the fringe to the rough...