Looking at some results for this...
Matt Ginella has a TGC video that the top AP courses you can play (in order?) are The Bog in Wisconsin, Deacon's Lodge in MN, the Bay Course at Kapalua and The Palmer Course at Turtle Bay in Hawaii, and Bay Hill.
Golf.com has a top 10 gallery of Arnie's course at Reunion in FL, Turtle Bay, Hiddenbrooke in CA, the Old at Half Moon Bay, Palmer course at La Cantera, Deacon's Lodge, Bay Creek in VA, Running Y Ranch in OR, Teton Pines in WY, and Tralee.
Links Mag has a Top 10 AP courses you can play, which adds Semiahmoo, Oasis GC (Palmer), Aviara, Stonewall in WV, and the K Club to the discussion...
Among those I have played, I liked Tralee, Bay Hill, Mid-South, GC of New England, Lonnie Poole and Laurel Valley all on some level. GC of NE is probably the best of the bunch, although Tralee is up there just by where it is located.
Of the other Palmer courses I have played, two were totally re-designed (TPC Boston by Hanse and Broadmoor-Mtn. by Nicklaus), one is NLE (Grenelefe East), and the others are uninspiring (Eagle Ranch and Lost Tree in CO, The Carolina in Pinehurst).