Specifically for the zoos you asked about that I've visited:
Toledo - Great Black-backed Gull, Southern Pudu, Kagu, Many-colored Fruit Dove, Golden White-Eye, Pink-necked Fruit Dove, Pesquet's Parrot, Raggiana Bird-of-Paradise, Golden-backed Woodpecker (only North American holder), Lesser Bird-of-Paradise, Egyptian Plover, Koala, Lowland Paca, White-headed Vulture (only US holder), Western Capercallie, Santiago Giant Tortoise (only North American holder), Harlequin Duck, Spectacled Eider, Long-tailed Duck, Japanese Isopod, Giant Isopod, sea spider species, Scaly-sided Merganser, Chestnut-breasted Malkoha, Australian Magpie, Blue-winged Kookaburra, North Island Brown Kiwi, Lake Erie Watersnake, Conant's Mushroom-tongue Salamander (only holder), several native salamander species, Coconut Crab, Ribbed Newt, Oleander Aphid, Anna's Hummingbird, Yellow-lipped Sea Krait (only North American holder), African Pygmy Falcon, Tasmanian Devil, Kodiak Bear, Maned Wolf, Tuatara, Saltwater Crocodile, Ornate Flying Snake, Greater Malayan Chevrotain, Flashlight Fish
Toledo is loaded with rarities, it's kind of amazing. These are only the species I *know* are rare, there's probably others they have that I am simply not aware of how rare they are.
Detroit - Titicaca Water Frog, Stout Salamander (only North American holder), Anderson's Newt, Mountain Chicken, several mantella species, Japanese Giant Salamander, Striped Newt, Narrow-striped Dwarf Siren, Kihansi Spray Toad, Wyoming Toad, White-lipped Deer x American Elk hybrid, Wolverine
Columbus - Moose, Wolverine, many species of US native birds (the only holder of a few species), Siberian Musk Deer, Golden-mantled Flying Fox, Pallas' Cat, Lake Erie Watersnake, West Indian Manatee, Bonobo, Black Duiker, Painted Stork, North Island Brown Kiwi, Southern Hairy-nosed Wombat, Feathertail Glider, Koala, Tasmanian Devil, Village Weaver, Markhor, Greater Malayan Chevrotain
Lincoln Park: Puerto Rican Parrot (only holder), White-lined Tanager, Collared Finch-billed Bulbul, Kagu, Cactus Mouse, Moholi Bushbaby, Klipspringer
Brookfield: Chinese Giant Salamander, Screaming Hairy Armadillo, Lowland Tapir, Klipspringer, Tree Pangolin (only ones on exhibit in the US), Texas Blind Cave Salamander, Gray Gull, Chicago Garter Snake, Masked Bobwhite, Home's Hinge-backed Tortoise
Shedd: Pacific White-sided Dolphin, Beluga, Flashlight Fish, Giant Isopod, Hawk-headed Parrot, many, many, many more
Milwaukee: Bonobo, Whooping Crane, Spangled Cotinga, Egyptian Plover, Madagascar Teal, Greater Malayan Chevrotain, Pale-mandibled Aracari, Thompson's Gazelle, Senegal Bushbaby, Common Vampire Bat
Indianapolis: Walrus, Crab-eating Macaque, Wild-type Helmeted Guineafowl, Great Green Macaw