Just revisiting this thread just to see how my list now differs from that of a year ago - tanks to recent research I like to think I know significantly more about the collections of the zoos in question at the very least...
I'll give reasons for each to explain my choices and preempt questioning. I have gone for collections that I think add something different to the zoo scene, whether that is in terms of collection, exhibitry or otherwise, so perhaps some of the less exciting but solid zoos will be missing. However, hopefully it isn't too contentious.
The collections that are italicised are those that would make it into my Top 20 and collections in blue are aquaria.
Austria
Alpenzoo Innsbruck - One of Europe's best at exhibiting the country's fauna, with some lovely exhibitry and rarities such as the Wallcreeper or Black woodpecker.
Reptilienzoo Nockalm - Certainly one of Europe's premier reptile collections, with a plethora of unique taxa, not least the Brown forest cobra and Rosario rattlesnake.
Haus des Meeres - This place outdoes Schoenbrunn in rarities, mostly due to its high fish and reptile count. One of the better aquaria in Europe overall, with a good collection of non-fish taxa to boot.
Tiergarten Schoenbrunn - One of the more famous European zoos for a reason - it comprises a wonderful collection housed in some of the most charming structures in any zoo, along with world-class zoo food.
Croatia
Zoo Zagreb - Deserves a mention on here for a fantastic collection, some nice exhibits and the only major zoo to have Olms.
Belgium
Zoo Antwerpen - A fairly old collection, with some beautiful buildings. The place also happens to have one of the most notable rarities in Europe - Amahoro the Eastern lowland gorilla.
Pairi Daiza - The zoo that likely most closely resembles places like Columbus across the pond, Pairi Daiza has some lovely exhibits, some awful exhibits and everything in between. Despite this inconsistency, it can't not be on this list.
Planckandael - Another very nice place with natural exhibits and a particularly nice European zone, certainly one of the best in Belgium.
Czechia
Zoo Brno - Great collection of mammals in particular.
Zoopark Chomutov - Another good collection and some nice exhibits.
Dvur Kralove - The best collection of African animals in Europe by a margin.
Zoo Zajezd - An very interesting place as it is the best collection for chameleons in Europe but is also impressive in other aspects.
Zoo Ostrava - Great collection but also home to some rather nice architecture.
Zoo Jihlava - A mammal collection that rivals that of Prague's and some very nice exhibits indeed.
Zoo Plzen - The best collection in Europe bar none, and one of the better zoos on the continent as well, Plzen harbours one of the greatest collections of rodents ever assembled and a plethora of species from every class.
Zoo Praha - Probably the best quality zoo in Czechia and a fantastic collection as well, with some major rarities and beautiful exhibits. One of the best in Europe for sure.
Zlin-Lesna - A good collection and generally good exhibits.
Denmark
Den Bla Planet - Probably the biggest aquarium in Europe in terms of collection, all in one of the most interestingly designed aquarium buildings on Earth.
Copenhagen Zoo - Only just scraped in but a good ABC collection with pandas and devils.
Randers Regnskov - A pretty interesting place pretty much entirely beneath three large domes, displaying tropical species.
France
Nausicaa - Holder of the only manta rays in Europe, Nausicaa is a bit like a scaled down Georgia Aquarium - one half is excellent and the other is mediocre.
La Vallée des Singes - A great place for primates, rivaling Apenheul.
Zoo d'Amnéville - Doesn't have a great reputation due to its tiger show but is of fairly good quality in general and has a strong ABC list.
Zoo Citadelle de Besancon - Perhaps a contentious inclusion but the format of the place is unique in Europe, located inside a medieval citadel, which makes for some interesting exhibits.
Bioparc Doué la Fontaine - The most interesting zoo in France, with a peculiar but wonderful taste in exhibit design. Home to some of the most brilliant exhibits on the continent.
Haute-touche - Best collection of deer in Europe and in massive fields roaming in semi-liberty.
Aquarium de la Porte Dorée - A massive collection with plenty of rarities but no real centrepiece. Perhaps a bit of a scaled-down Shedd type of place.
Zoo de Vincennes - Took an age to renovate but has turned into an impressive place with a good collection of birds in particular and some nice exhibits.
Menagerie du Jardin des Plantes - One of the oldest zoos in Europe and also one of the more interesting styles of exhibitry, often combining 19th Century cages and railings with more modern materials. A nice collection as well.
Parc des Félins - The best collection of felids on the continent, all in massive, naturalistic enclosures.
ZooParc de Beauval - One of the bigger zoos on the continent, with a nice collection, generally nice exhibits and rarities such as Harpy eagles and Douc langurs.
Germany
Tierpark Berlin - Neighbour of the slightly more talked about Zoo Berlin, this place is fabulous in its own right. It developed significantly during the Cold War and has not looked back since.
Zoo Berlin - Another competitor for best in Europe, Zoo Berlin has a massive collection, much of it housed in its Aquarium/Terrarium as well as some very nice architecture.
Tierpark Chemnitz - The best collection of amphibians in Europe.
Zoo Dortmund - Another nice collection with a good quality of exhibitry, along with being one of two collections in Europe with the Southern tigrina.
Zoo Dresden - Largely included on here thanks to its lovely European bird contingent.
Zoo Duisburg - Another nice West German zoo, known for being the home to the last specimen from the Iniidae in Europe.
Aquazoo Dusseldorf - Were it not for Berlin's Aquarium, this would probably be Germany premier aquarium/terrarium, with a massive collection of fish.
Zoo Frankfurt - Another wonderful collection, with lots of unique species as well as lots of history.
Tierpark Hagenbeck - As the name suggests, the first place to widely use moats to create a more naturalistic environment for the animals.
Zoo Hanover - Like Pairi Daiza, quite similar to the American approach to animal exhibitry at times, with a large themed Arctic area in particular.
Zoo Karlsruhe - An all-round decent place.
Zoo Koln - Outstanding collection, rivaling that of both Berlins and Prague, this place is particularly known for its waterfowl and fruit-doves.
Zoo Krefeld - Yet another middle-of-the-road sort of place but with a massive rarity - the only Mountain anoa in captivity.
Zoo Leipzig - Home to another of the biggest rarities Europe has to offer, the Chinese pangolin. This place has lots more besides - a large tropical greenhouse, a wonderful ape complex and a good standard of exhibitry throughout.
Zoo Magdeburg - One of the better small carnivore collections out there along with some nice exhibitry.
Tierpark Hellabrunn - A historic zoo, laid out in a fairly taxonomic format. Not as many rarities as one might expect but the quality of exhibitry is generally high, making it one of Germany's best zoos.
Allerwetterzoo Munster - An excellent collection, particularly in regards to reptiles (specifically Asian box turtles) in which in appears to specialise.
Tiergarten Nurnberg - Consistently excellent exhibit quality and a great collection.
NaturZoo Rheine - Criminally underrated place that is rarely talked about on here despite its excellent exhibitry and collection.
Wilhelma - One of the more old-fashioned zoos in Europe with a nonetheless great collection and mostly good exhibitry.
Walsrode - Needs no introduction here.
Zoo Wuppertal - The only Indian leopards in Europe among other things.
Hungary
Budapest Zoo - The best collection in the country and one of the older zoos in Europe.
Sosto Zoo - Touted by many to be better than Budapest, with a decent collection and generally good exhibitry.
Italy
Oasi di Sant Alessio - Fabulous collection of birds and very interesting place in its own right. Probably the most intriguing zoo in Italy, at least for me.
Parco Natura Viva - A mainly ABC collection but good quality of exhibitry in general it seems and probably on balance the best zoo in Italy.
Netherlands
Artis - Some nice species and nice exhibitry, along with a fair bit of history make this an interesting place, though its popularity is probably enhanced by its location.
Apenheul - One of the best zoos for primates in the world, formerly holding Proboscis monkeys. Now not such an impressive collection but very nice exhibits nonetheless.
Burgers Zoo - One of the zoos with the best exhibitry in Europe on the whole, with magnificent greenhouses and some very nice outdoor exhibits.
Safari Park Beekse Bergen - A nice safari park with good quality of exhibitry but not many rarities.
Ouwehands - Notably holds pandas but has a fairly good quality of exhibitry and a few rarities up its sleeve.
Rotterdam Zoo - A zoo that is currently in a bit of a stasis - it hasn't really developed much in recent times, yet is still a great place with some fantastic species.
Poland
Zoo Plock - Poland's third best collection on the whole, with a large number of fish and herps.
Poznan Nowe - Large mammal collection with a number of rarities and slightly lacking in other classes but still one of the top zoos in Poland.
Warsaw Zoo - Probably Poland's second best zoo on the whole, with a nice collection of birds in particular and nice exhibitry.
Zoo Wroclaw - Poland's best zoo and one of the best collections in Europe. Not so many birds or mammals but it makes up for this in herps and fish, as well as some great exhibits, not least the internationally renowned Afrykarium.
Portugal
Vasco de Gama Aquarium - One of Lisbon's two great aquariums. It is located in a very nice yellow building and has a good standard of exhibitry.
Lisbon Oceanario - Another great aquarium in the heart of Lisbon, this time out on the ocean and in a modernistic yet interesting building. It holds a great collection as well as more nice exhibits.
Lisbon Zoo - Slightly better in exhibitry than Madrid or Barcelona, so I've decided to include it. It holds Iberian lynx along with lots of other nice rarities.
Russia
Moscow Zoo - Magnificent collection, though not always exhibited in fantastic conditions.
Moskvarium - The best aquarium in Russia from what I've heard, with a massive collection of fish in particular.
Tula Exotarium - A massive reptile collection with countless rarities.
Spain
Cabarceno - One of the most scenic zoos in the world, with the park hugging the sides of massive cliff formations.
Madrid Faunia - Very nice but slightly random collection - the more interesting of the two Madrid zoos.
Bioparc Valencia - Quite elaborately themed throughout the park but a very good representation of the African continent whatever your views on its style of exhibitry. Some very interesting mixes as well, with Pygmy hippo-sitatuga-drill coming to mind in particular.
L'Oceanografic - One of Europe's best aquariums for sure, with unique and in my opinion very aesthetically pleasing architecture and a wonderful collection.
Loro Parque - The best collection of parrots in the world, quite simply.
Sweden
Zoo Kolmarden - A great place, with a large ABC collection and great exhibits all round.
Boras Djurpark - Contains one of the best african savannas in any European zoo.
Nordens Ark - Large and covered in pine trees, with generally fantastic exhibits.
Switzerland
Zoo Basel - A great collection and consistently fantastic exhibitry.
Tierpark Dahlholzli - Great European collection and good exhibitry.
Aquatis Lausanne - The biggest collection of freshwater fish in Europe in an incredible building.
Zoo Zurich - Home to some of the best exhibits in the world including Masoala, a large tropical greenhouse as well as a beautiful elephant house and a spectacular Spectacled bear exhibit.
UK
Bristol Zoo - Unfortunately announced it was closing and moving to its sister site outside the city, Bristol has an excellent quality of exhibitry and a nice collection.
Crocodiles of the World - Perhaps contentious given the omission of Eskilstrup and Protivin but I think it is deserving of a place in the top 100.
Chester Zoo - No explanation needed here.
Colchester Zoo - In my opinion quite underrated, with a generally excellent quality of exhibitry and a few nice rarities as well.
Edinburgh Zoo - On the way down but still has some fantastic exhibits like Budongo and continues to draw in lots of visitors, so I think it deserves a place.
Highland Wildlife Park - One of the most interesting places in the UK, it has a consistently high standard of exhibitry and is home to some of the best exhibits for certain species on the continent.
London Zoo - Contentious perhaps, but while London has somewhat fallen since its golden age(s), it continues to have a good enough collection and standard of exhibitry (as well as all the history of course) that I think it warrants it.
Cotswold Wildlife Park - Another rather charming place with a fairly long species list and some very nice exhibits up its sleeve.
Slimbridge WWT - A massive collection of waterfowl but also great for spotting wild birds.
Hamerton Zoo - One of the most intriguing collections on the whole, with a superb array of Australian (in particular) species.
Paignton Zoo - Formerly one of Europe's premier primate collections, Paignton is still very good with the aforementioned order, and has a fairly good collection otherwise.
Twycross Zoo - Fairly good collection and standard of exhibitry.
Scottish Owl Centre - Best collection of owls in Europe, possibly the world.
Jersey Zoo - Founded by the late Gerald Durrell, this place has a consistently great quality of exhibitry and is heavily involved in a number of conservation efforts around the globe.
Whipsnade Zoo - Large zoo with pretty much all-round great exhibits and some nice species in there too.
Hopefully this isn't too contentious
.
Both are on the list.
