I personally really like Burgers' Zoo, GaiaZoo and Safaripark Beekse Bergen, and I think they are three high-class facilities.
I am also very fond of Zoo Planckendael as it is my home zoo and the zoo where the love of and interest in animals, zoos and science all began for me. It is a decent zoo that is not without imperfections, admittedly, and perhaps not the greatest, but to me it is still a cool place that I have a special fondness for, partially because of personal nostalgic reasons.
I also have to name Pairi Daiza here. In terms of sheer impressiveness and at times outright over-the-top craziness this zoo is hard to beat in Europe I think. And while Pairi Daiza has several major and minor shortcomings that have discussed here at ZooChat before, the fact that a two-day visit (with a stay in their resort) now seems to be becoming a yearly tradition for us, does indicate that I like the place and would rank it quite high. Also, the collection they have on display is very impressive and worth a visit in itself.