Hmm, this is a hard one, because there are so many and they're all so great. I'm actually going to go as far as making a top 12, as this will include most German zoos I have visited and thus give a better total view of my opinion.
1) Zoo Leipzig.
A very beautiful zoo that manages to follow the modern trend of bigger, more immersive exhibits and themed areas to please the general public, but still has plenty of
very rare species to keep it more than just 'interesting' for the hobbyist, like us. A very comprehensive map, guide published yearly with full inventory list, and very friendly and approachable staff make it so this zoo is all the way at the top.
And, well, there's Gondwanaland, which is just absolutely fantastic.
2) Zoologischer Garten Berlin.
A very typical city zoo (which I love) with plenty of intriguing architecture, a very extensive history, and a lot of magnificent species to tie it all together. Plenty of oddities found nowhere else, in mostly wonderful exhibits.
3) Weltvogelpark Walsrode.
A collection I haven't actually visited myself, but I know enough about the wonderful species to know that it's a park I absolutely need to visit, and need to visit soon. From pictures, most of it looks fantastic as well!
4) Tierpark Berlin.
A very nice collection with a lot of very nice species in very nice and spacious exhibits, but in my opinion it misses something to really draw attention? While there, I felt more like I was just ticking off things from a list over actually enjoying seeing the animals; not that I didn't, but not many exhibits individually were very eye-catching in my opinion. Regardless, the Alfred-Brehm-Haus and Elephant house are extremely impressive works of art with some very nice species.
5) Zoo Frankfurt.
Night houses are my all-time favorite areas in zoos, and guess what zoo has the biggest in the world? You guessed it. Besides the absolutely wonderful Grzimek House, it also has a plethora of other absolutely wonderful buildings and exhibits; and a beautiful entrance!
6) Kölner Zoo.
The German zoo I've actually visited most of all (though still only a measly 3 times!), and still absolutely love. A very stereotypical 'German' zoo with a lot of wonderful history, and a plethora of very impressive buildings with many nice species.
7) Zoo Wuppertal.
My love towards cotingas probably pushes this one forward a little, as without the bird house I don't think it would make the top 7, but again, a wonderful zoo. Besides the bird house other very nice exhibits are the gigantic area for lions, and, of course, the only Indian leopards outside of Asia.
8) Zoo Duisburg.
I found it very tough placing this one somewhere on this list, as it was the first German zoo I visited and I don't quite remember everything so well. Obviously there are some incredibly inspiring exhibits (mainly the Rio Negro exhibit coming to mind, of course) that make the zoo very attractive, but as soon as that last river dolphin individual will pass away I would need a very good reason to revisit again; a lot of nice species, but a lot of the exhibits (in my opinion) weren't what they could be. However, this might all be because I visited very early on in the year, I'm sure in the summer it looks better (as do most zoos).
9-12) Zoo Dortmund / Wilhelma Stuttgart / Zoo Magdeburg / Tierpark Hagenbeck Hamburg.
4 Collections I haven't actually visited myself, thus don't quite know where to place them, but I am positive that if I were to visit them, they would certainly be somewhere in the top 15. The first three have some very nice species going for them and the last has had a very dramatic impact on the history of zoos as a whole, which is why I'm also including it in here.
Not included but zoos I have visited are Alwetterzoo Münster and Tierpark Nordhorn; very nice zoos, and the former has a very interesting idea behind it that I think could/should inspire many other parks, but in totality they just don't jump out enough to quite make it into this list.
As with all "top X" lists, mine should be taken with a grain of salt, as I've only visited most of these collections once and a lot depends on the weather, no-shows of highlight species, how crowded everything is, etc. I also find it very hard to place certain very similar zoos above or below each other, as I thoroughly enjoyed visiting all of them.
