On first thought, I'm definitely having an easier time coming up with courses where the whole is less than the sum of its parts than more...
Some of the courses mentioned above are interesting because to me, they show how when a course is excellent and very consistent, we might overlook how great some of the individual holes are. Ira Fishman mentions Pinehurst no. 2 and St. George's Hill. I think that they both fit this category. They're both very strong, consistent courses--among the few I've played that have no bad holes and arguably no indifferent ones.
But I also think that they both have great holes. The opener on no.2 may be the best that I've seen and the following two are world class. I think that at least 5, 8, and 14 are also among the best holes that I've played. Same at St. George's Hill. In addition to the aforementioned 10th hole, I'd note 8, 16, and 17 as great holes. Now they may not be on the same level as St. Enodoc 4 or Cypress Point 16, but almost nothing is. Very few courses--even great ones--have holes of this caliber.
But I think that we might overlook the greatness of some of these individual holes because it's true for both that the course overall is so strong and so consistent that that's the main thing we take away. There are a few great ones but they don't peak so far above the rest--the variance in the quality of the holes is still low and that's what we take away from the course. And I don't think that's wrong, but I do think that it may be causing us to overlook the greatness of some of the individual holes.
Some great courses clearly don't fit this category. They have great holes but higher variance. St. Enodoc, I think, is one. The 4th hole stands out, but there isn't another hole that I'd take above the no. 2 and St. George's Hill holes that I mentioned. And the weakest holes there are weaker than anything at no. 2 or St. George's Hill.
Of course as Sean Arble has mentioned, St. Enodoc may be greater than the sum of its parts for a different reason: that the course uses its diverse landscape in an especially interesting way.