they've been mentioned a million times and won't be new to most zoo fans, but a thread like this should have the
Gelada/ibex/hyrax exhibit at Bronx.
Masoala Hall for Malagasy animals at Zurich.
Vulture aviary at Tierpark Berlin.
Kelp forest aquarium at Monterey Bay -- one could argue that it doesn't qualify for 'unique' as other aquaria have kelp tanks. However, overall none are as remarkable as the one at Monterey (size+lush kelp), even if South Africa's Two Oceans is fairly close.
Coral reef aquarium at Burgers' -- probably the nearest to a
complete coral reef ecosystem created anywhere outside the tropics in a
single tank: fish, invertebrates, corals that have spawned repeatedly; the coral growth has even allowed them to add a few corallivores.
Polar bear exhibit at Skandinavisk Dyrepark -- this was the largest and arguably best (some would probably rate Detroit's higher due to their underwater viewing) polar bear exhibit in the world until recently when apparently surpassed by
Orsa Bjornpark. However, since I haven't visited Orsa Bjornpark my judgement of that park is entirely based on what I've read and seen on photos; they are aided by the cold location. Their Siberian/Amur tiger exhibit looks remarkable too. I'll leave it to others to judge if the exhibits at Orsa have too many components used at a smaller scale elsewhere to qualify for 'unique'