Mine I rate purely on my experience of being in them. A lot of these I remember walking through and having a sense of wonderment because of experiences with the animals, the collection on animals, the display, and most of all the narrative that takes place throughout the exhibits.
1) Jungle World - Bronx Zoo - Despite being indoors, I was completely blown away by Jungle World. The amount of fabrication that went into it was immense and the narrated movement between various types of habitats. There are a few husbandry issues with the exhibits, but the movement from light to dark as you walk through the set of exhibits really sets the experience, especially how well the approach of each exhibit area is set up.
2) Northern Trail - Woodland Park Zoo - Great line up of North American creatures. Every habitat is exceptionally well done for the residents inside of it, there are multiple panoramas as well. I remember being amazed that the Grizzly Bears seemed like they were on a rock above me and seemed to be free of any exhibit.
3) Oklahoma Trails - Oklahoma City Zoo - Exceptional series of exhibits for local animals and local habitats. Because of this, the landscaping is very well done. Great exhibits for every animal, a mixture of exhibit types (ex: mixed exhibits, hoofstock, carnivores, aquariums, amphibious exhibits, nocturnal house) that all reflect local ecological prowess.
4) Asia Trail - Smithsonian's National Zoo - Great series of exhibits, hardscaping structures are well built, have a unique style. Some of the exhibit structure are rudimentary (glorified moats, indoor housing), but great selection of animals and landscaping. (mixing of Thuja occidentalis and Cryptomeria?) Infrastructure and off-exhibit holding is well organized.
5) Kingdom of the Night - Omaha Zoo - Wonderful series of nocturnal exhibits. Fabrication of the cave is the best I have ever seen, lighting is very well done, especially in the swamp section. Great collection of species.