While a lot has already been said by
@lintworm, I also want to make a case for Burgers' here (even though I haven't visited Wroclaw yet and I'm obviously biased

).
Ectotherms is probably the last category you would think of when considering the strengths of Burgers', but I think it still has a lot to go for it, even though it might not always be obvious at first sight, both in species present and in the way they are exhibited.
So let's start with the reptiles and amphibians. This group is one of the most underrepresented groups in terms of number of species at Burgers', but they still hold some rather nice species in good enclosures. For example, the rattlesnake species Burgers' holds (
Crotalus ruber) is only kept at two other public collections in Europe and the exhibit they are in, with the campsite and the peccary enclosure backdrop, makes for a unique display. The other "enclosed" reptiles and amphibians, like the Indian water monitors and reticulated pythons in the Rimba, the gilamonsters and Colorado toads in the Desert, the green tree pythons in the birdhouse and the tortoises, turtles (who make for a great display on the beach with the capibara and whistling ducks) and caiman in the Bush, are all kept in spacious and good looking enclosures. A real strength of Burgers' on reptile- and amphibian-terrain are the free-ranging species. There is something really special about turning a corner in the Bush and suddenly seeing a huge male green iguana crawling out of the undergrowth, or spotting one of the hundreds of Guadeloupean anoles (kept in only one other public collection according to ZTL). The Montserrat whistling frogs are hard to spot due to their small size (I doubt if they would be easy to spot in a more conventional exhibit), but they certainly are present and can be heard when walking through the Bush late in the afternoon or when the zoo is open in the evening.
Fish are a group the zoo has a lot more species of, and I consider saltwater fish a real strength of the zoo. Burgers' Ocean is ofcourse the largest and most obvious display of fish in the zoo, so let's start there. The Ocean is themed as if it was the journey of a diver through a coral reef somewhere in the Indian/Pacific Ocean, starting at the beach and than slowly progressing through the lagoon, to the inner reef, than the outer reef and ending at a harbour. Burgers' keeps a huge collection of reef fish, both large and small. The obvious stars of the aquarium are the cartilaginous fish, of which they keep such species as scalloped hammerhead, blacktip shark, giant shovelnose ray, epauletted shark, blue-spotted stingray and spotted eagle ray. The bony fish department is ofcourse also really good, but I know too little about fish to comment on rarity of species. The real strength of the Ocean are the displays. I don't know of an aquarium in which the displays give such a good image of the ecosystem they are displaying as here. I could spend hours at the living coral tank and discover something new everytime, for example the huge shoals of cardinal fish living between the coral, or the gobies on the floor of the tank, or the sight of a stingray slowly gliding over the coral or...I could go on for sometime, it is simply an amazing display.
The freshwater fish in Burgers' are a little less obvious than their saltwater counterparts, but the zoo still keeps some interesting species. There are for example the freshwater rays and redtail catfish in with the caiman, the pacu in with the capybara and the tilapia in one of the streams in the Bush; and there are the already huge shoals of South-American fish in with the manatees in the Mangrove.
And finally there are the invertebrates. They are not always obvious, but Burgers' still keeps quite an impressive collection, mainly in the Ocean. There, the huge amount of living corals, sea urchins, anemones, sea snails, shrimps, sea cucumbers and other lower animals are a very important part of the displays and I think it is a real strength of Burgers' that they also give these animals the attention they deserve in the signage. Burgers' also does a huge amount of scientific research on the biology and breeding of corals (and also the breeding of coral fish) together with several Dutch universities. Other obvious invertebrates in the zoo are found in the Desert, with displays for tarantulas, scorpions and cave crickets, and in the Mangrove, where the mud flat with the fiddler crabs and horseshoe crabs makes for a unique and very entertaining display, together with the large number of butterflies. Invertebrates that are less obvious are found in the Bush, where the ants, millipedes, cockroaches etc. are a very important part of the ecosystem, even though visitors will probably never see them.
All in all, I think that while Burgers' is beaten on size and comprehensiveness of it's reptile and amphibian collection, it is as good or better than Wroclaw in the saltwater fish and invertebrate departement, and I think Burgers' deserves extra points for the uniqueness of it's displays. So in the end, I think Burgers' should win this.