Some favorites include:
2 at Seven Oaks. This is a neat short par three (unusual for Robert Trent Jones), so it is usually nothing more than a mid-iron for me. YOu can't see the putting surface, but you have to know where the green is because missing the green is deadly. The hole probably contains the most severe green in Western New York, and you can make a 2 or a 7 with ease.
2 at Irondequoit Country Club. This hole is longer than the above hole at 170 yards. It has no bunkers, but the green is elevated steeply above the player. Interestingly, the hole is relatively flat until about 30 yards short of the green. It has a huge, rippling green that allows players to hold longer irons on the green and makes putting difficult. Mark Chalfant included this hole on his "Ultimate 18" a couple weeks ago, so he can speak to the hole's greatness.
17 at Long Shadow! Many people have discussed and praised this hole. The massive punchbowl green makes this long par three eminently fair. Just don't go long!
9 at Leatherstocking. This hole is a tremendous reverse Redan-style par three. The hole appears wedged into the routing, but it is one of the absolute best on the course. It is part of a killer set of par threes. The green is benched into a hillside, meaning that there is tons of hill left to knock golf shots onto the green. Of course, this also means that right of the green is DEAD. It's a hole where you have to trust your swing and hope for the best.
From the diverse lengths of the three holes mentioned above (140-200 yards), I conclude that a steep hole par three can be great regardless of the length of the hole. The key component to designing an uphill par three is designing a green that will hold golf shots hit from the length of the hole. The architects on each of these four holes (RTJ, Ross, Mike Young, and Devereux Emmet) do this very successfully.