I have yet to design a par-3 course. Maybe, someday.
Coore and Crenshaw have done a lot of them ... Friars Head, Austin, and Colorado G.C. have already been mentioned, and I think they did a couple more as well. Actually, Bill also did one at Golf du Medoc in France, although when I went to see it a couple of months ago, half the holes had been abandoned.
I do wonder how much play any of these facilities really get. I've been on the Cliffs course at Olympic three times, and only seen one golfer. I've been to Friars Head four times, and never seen anybody playing the par-3. The most utilized one I know of is Augusta National -- in fact I played it in January when I was there.
The one which has yet to be mentioned is Tom Simpson's par-3 course at Morfontaine in France, which I somehow didn't see when I was there. Everyone says it has the coolest set of greens you can imagine.