@ANyhuis
As you have mentioned above (and I absolutely agree with you ) Prague Zoo is the best in my country, with fantastic collection of animals (Checkered Elephant Shrew, Ratel, Chinese ferret-badger, 2 species of Cloud Rats, Gharials,Shoebills etc), my second favourite zoo is Pilsen, because of a big variety of small mammals that cann be seen in Madagascar Pavillion and Night of Africa House, which is divided into day a night section. Last year they finished new African and Asian areas, both are really worth seeing.
Lesna is situated near the Slovak border and is a bit out of hand but located in the beautiful environment, the whole area is divided into zoogeographical sections, most animals are kept in large and natural enclosures, the animal's collection is not so big but you will be intrigued with this beautiful park, especially the new-built area called Etiopie will catch your eyes and Yucatan tropical hall attracts attention of many visitors too.
Dvur Kralove was my prior Number 1., but this zoo has lost its former fame and charm, it has became too much commercial. Dvur still has the largest variety of african ungulates in Europe, but the collection was much better in 70-80-ies, with 6 species of hartebeests, bushbocks, gerenuks...but it was not possible to import new animals or get new blood from other european collection because of rarity of many species, so they have gradually died out. But still one of the best Czech's zoos, can be far more ahead with right person on director's position...
Regarding at my opinion, these are the best Czech zoos and I am pretty sure, you will be satisfied with these collections