Forgot that I had already posted on this thread, and when I found my previous list, I wasn't too happy with both the order of it and the explanations I provided.

Couple that with the fact that I have visited a few new top ten contenders since, and I feel an update is necessary, this time trying a new format.
For what it's worth, I have visited 58 zoos in total, granted that I am using a fairly generous definition of 'zoo' to get the above number (for example, aquariums within museums are included, but farms or other domestic-centric places are of course not).
My top ten favourites, if I allow myself to show bias towards zoos that I have a strong sentimental connection with, although there are other reasons that I may take to a zoo more fondly than another, of course:
1. ZSL Whipsnade Zoo (very close to my heart)
2. ZSL London Zoo (sentimental connection and Blackburn Pavilion)
3. Zoo Zurich (amazing exhibits, brilliant ambience with futuristic buildings and good conservation links)
4. Prague Zoo (pangolins, birds-of-paradise and gharials with many nice aviaries)
5. ZooParc de Beauval (first world-class zoo I visited when I was quite young, so an emotional pick)
6. Exmoor Zoo (rare species, beautiful location, many visits)
7. Tierpark Hagenbeck (great to be immersed in the history, and to see a walrus)
8. Zoo Dresden (exceeded my low expectations, great exhibits and a homely feel)
9. Oceanopolis Brest (first world-class aquarium I visited, so a very exciting experience for me)
10. Antwerp Zoo (beautiful architecture and the Eastern Gorilla)
Honourable mentions should go to the following, roughly in order of how close they were to making the cut:
Highland Wildlife Park - gorgeous setting, good specialist focus and amazing enclosures
Shaldon Zoo - very charming
Parc Zoologique de Paris - my first manatee
Horniman Museum - close to where I live so countless visits over the years
Chester Zoo - very high quality of enclosures, could be top ten without some key exhibits closed
And here is my attempt at making a list of the top ten best that I visited. What I mean by this is not that this is the objective list (I believe there is no such thing), but that I wasn't taking sentimentality into account and was ranking solely on quality, which in and of itself is a subjective thing and quite difficult to define.

But, using my own definition of quality with regards to zoos, here are the 'best' that I have visited:
1. Prague Zoo
2. Zoo Zurich
3. Burgers' Zoo
4. ZooParc de Beauval
5. Chester Zoo
6. ZSL Whipsnade Zoo
7. Antwerp Zoo
8. Zoo Dresden
9. Highland Wildlife Park
10. Cotswold Wildlife Park
For what its worth, deciding between Prague and Zurich was all but impossible and a decision that I have been reversing just about daily in recent times. Leaning towards Prague at the moment, but tomorrow (or in a few minutes, for that matter) my answer could be different. That doesn't just apply to the above list. Even ignoring quality and judging it solely from enjoyment on the previous list makes the decision difficult.