Those who live in Europe are best qualified to answer. However I have made five trips there (most recent last month) and have visited zoos each time, though not as many last two trips as my interest in zoos is waning. I will list the ones I have personally visited in order of preference, as in the first on the list is my favorite, then second favorite and so on. Please note my preferences are based on wild cats, large mammals, large enclosures and photo opportunities. Some that I list near the bottom would be listed near the top by others due to their history or variety.
Le Parc Des Felins (France)
Heritage Wildlife Foundation (England)
Highland Wildlife Park (Scotland)
Chester Zoo (England)
Rare Species Conservation Centre (England - now closed)
Port Lympne Wild Animal Park (England)
Langenberg Wildlife Park (Switzerland)
Zoo Salzburg (Austria)
Zoo Zurich (Switzerland)
Edinburgh Zoo (Scotland)
Zoo Vienna/Schonbrunn (Austria)
Parq Zoologique Du Paris (France)
London Zoo (England)
Howletts Wild Animal Park (England)
ZooBotanico Jerez (Spain)
Le Menagerie (France)
As I said my preferences are very specific and other considerations (history, etc) would change the order. I am sure there are people reading this who are yelling at their screen and wondering what kind of idiot would place Heritage Wildlife Foundation above London Zoo or Schonbrunn.