Some great par-3s on courses we don't talk about too much:
Orchard Lake - Hole 7, 13. 13 in particular is fantastic use of land with the green perched above a 30 foot dropoff to the right of the green.
Carolina GC - Hole 3 - Long and hard, with clever bunkering and a very difficult green. Not entirely unique to Ross, but a very good hole.
Sebonack - Hole 12. The downhill version of Shinny's 11th, but with water in the background.
Dormie - Hole 12. 110 yards, with a unique tee box and a green that is subtle but oh so difficult.
... there are lots more