An interesting topic. Just want to emphasise that this is my own personal opinion.
Major Zoos
1. Taronga Zoo
Pros: A fantastic nocturnal house with around 20-25 nocturnal species including the long-beaked echidna, phascogales, bandicoots, gliders and all those other wonderful nocturnal gems. The bird aviaries are brilliant with a good range of native and Asian species. A well-designed reptile house with approximately 55 exotic and native species on display. Beautifully-done enclosures for several species like Francois Langur and Fishing Cat. The chimpanzee enclosure is excellent as well.
Cons: Lack of primates. Cramped enclosures for megafauna like the pygmy hippos and elephants.
2. Adelaide Zoo
Pros: Probably houses the best collection of birds of any of the major zoos. Nocturnal house and reptile house also look very nice. They hold several interesting species – Mandrill, Dusky Langur, Malayan Tapir, Colobus and in the near future (hopefully) bushbabies. This zoo could possibly move to number one on my list.
Cons: Some of the enclosures look quite dated (sea lion pool, lion enclosure) however their masterplan looks promising.
3. Perth Zoo:
Pros: Numbats and another fantastic-looking nocturnal house. The Asian Rainforest and African Savannah look nice as well. Perth Zoo also participates in several conservation projects with locally-unique species like the aforementioned Numbat, Western Ground Parrot, Dibbler etc.
Cons: They seem to have a smallish collection of birds compared to the others mentioned.
Small Zoos
1. Darling Downs Zoo
Pros: I may be a bit biased because it’s one of my local zoos.

A well-rounded collection with several regional rarities. The zoo has imported countless of species and is developing into one of the best (if not the best) zoo in Queensland in my opinion. Sri Lankan leopards will also certainly be a big milestone. A nice bird collection with a good range of pheasants, waterfowl, parrots and softbills. Reptiles are also represented with a solid range of species with a greater emphasis on the exotics to complement each of the four geographical areas.
Cons: I don’t visit the place often enough!
2. Hunter Valley Zoo
Pros: Very similar reasons to Darling Downs. They have also received several new species over the years (binturong, red-handed tamarin, Bolivian squirrel monkey, zebra etc). They also seem to have well-rounded bird and reptile collections. A zoo to watch out for over the next couple of years.
Cons: Cannot think of major ones.
3. Mogo Wildlife Park
Pros: A great range of primates including Javan gibbons (a favourite of mine) and (hopefully) a breeding group of gorillas. The enclosures look excellent especially for some of the smaller primates.
Cons: Lack of anything that isn’t exotic mammals.
Honorable mentions: National Zoo and Aquarium, Tasmania Zoo, Gorge Wildlife Park, Altina, Billabong Zoo and Wildlife HQ.
Something else to consider are the best native fauna parks for which there are several top-notch facilities. Places like Cleland, Moonlit, Currumbin, Healesville, David Fleay and Featherdale all spring to mind as fantastic places.
Due to aquariums being dominated by the Sea Life chain, there isn’t much to compare and contrast. Cairns Aquarium does look excellent though.