The funny thing in evaluating golf holes is that if you ask someone what the best hole on the course is, the answer, 99% of the time, is their idea of the worst hole on the course, or the one they like least. Try it.
I've had clients tell me the entire course I designed for them was much better than what they thought they were getting (usually on a public course commission) even using the term "You sandbagged me!"
Over the last few days, I have struggled to think of an individual hole that came out better than I personally expected, but I am sure there are some. I will echo TD's comments about sometimes thinking that the best natural hole doesn't need as much work. At the first Giant's Ridge course, they did favorite hole surveys (no the answers weren't "all but hole X..." as per above) and I was surprised that some of the holes on lesser land and woods, where I did do more bunkering came in almost universally as the favorites.
The other ones that I sometimes have a bit of sense of relief on are those up and over holes or other landforms that tend to create blind holes, and I am never quite sure if the planned earthworks will look good and fix the problems.
On the technical side, LOL, I recall that same Giant's Ridge course, built over a rock pile, and really fretting all winter that the subsurface flows were going to suck the topsoil down and out, leaving a field of craters the next spring. Thankfully, it didn't, even though you can still hear the subsurface river running under the 7th fw. At Superior National, the 7th there also required a steep, 30 foot high, rock-covered fill, on a 1 to 1 slope to widen the fw. At the bottom was a protected trout stream, which engineers at the adjacent ski hill had been fined for sullying. That said, it has held up quite well.
At Tempest, in East TX, I designed a valley par 3, and just assumed we could get the path down there somehow. Turns out, it took a 40 foot high bridge to cross that sucker, and oddly, riding high over the rushing stream turned into a nice view that golfers seem to love, so I consider that a happy (if expensive at about $100K) accident.