Bayonne by far, in my book. It remains Golf's greatest pottery experiment and a prime example of a shrewd golf developer actually being paid to dredge the adjacent harbor and use the material to shape a links course.
If sand-capping a waste area besides a body of water qualifies, then Ferry Point deserves a healthy mention. Nicklaus' team did a fine job with a flat site and to everyone's credit, it plays far more like a links course than say a Whistling Straits, or its cousin, The Irish Course. The latter Dye pair are effectively aerial course.
Lastly, although it doesn't play nearly firm enough to be considered a true links, I'd add Kiawah Ocean to the list as it was surely constructed along those lines. Come to think of it, I can't name any Pete Dye course that really plays anywhere close to a links.