I'll start in my own "neck of the woods" with the following ...
1). Maidstone
Wonderful holes in spots but not close enough to be mentioned as a serious top 100 course. Gets plenty of "in the hood" points with Shinny and NGLA being so nearby. Love the par-4 9th and a few of the other holes closer to the ocean but in sum there's little real depth or consistency to merit such a lofty position.
2). Bethpage Black
I say this with a heavy heart since I've played the course for well over 30 years and 200+ rounds. BB has become nothing more than golf equivalent of Barry Bonds. It has become the poster child for muscular golf with nothing more than added tee boxes -- I'm waiting for a tee box to be extended to Jersey for even more length.
BB doesn't have any real unique short holes because the desire to lengthen and narrow everything has become a mission unto itself.
It would help immensely if the course returned to a more "worn" or "natural" look instead of being so clean and country club looking.
3). Baltusrol / Lower
On the plus side it helps to have the name Jack Nicklaus on your roster twice as champ ('67 & '80 US Opens). Doesn't hurt that Lefty also won the PGA there.
On the flip side the layout is really a bore. There isn't anything memorable about it. I also see the par-3 4th as a tad overrated. Kudos to the club for keeping their profile in the mix but if people see this as a top 100 layout then they really need to play a good mixture of other courses that have not flown as high on the radar screen.
p.s. Although I have confined myself to my area -- I have to say Shoreacres would also be on my listing of heavy disappointments -- for Raynor fans the work he did at Camargo and Fisher's Island is good way beyond that of the Chicago-based layout.