Brad,
I am stretching your topic to the world top 100 in some of the responses below but here it goes:
1) I love links golf. The fact that Rye and Waterville aren't in there is a mystery as they are both very hard courses in relation to par, a factor that usually is helpful in getting courses included.
2) I love courses that are different and unique so the fact that Westward Ho!, St. Enodoc, North Berwick, Royal Ashdown Forest, Prestwick, Brancaster, Yale and the Plantation Course at Kapalua aren't in there is disappointing (though understandable, even if you don't agree).
3) I love Stanley Thompson's work and think his Famous Five should all be in the world top 100.
4) I love heath golf and think that courses like West Sussex, St. George's Hill, The Addington, and OF COURSE Swinley Forest should be in.
5) Several clubs - like Fenway with Hanse, Yeamans Hall with Doak, Plainfield with Hanse and The Ocean Course at Kiawah with Dye - have done or are in the process of doing very good work to their already excellent designs. Such courses deserve to go from the US Top 100 to the World Top 100.
The above are personal biases that yield an eclectic list. Given the diversity of courses (!) around the world, what a boring waste to see any ranking that has a preponderance of any one particular type course (i.e. "championship courses" for instance).
Cheers,