Interesting thread! I'll list my "zoo crawls" here as well.
WILD LIFE Sydney + SEA LIFE Sydney: These two are really practically made for visiting together - two fairly small collections that display a large range of Australian fauna, are located right next to each other, have late opening hours and if I recall correctly combination tickets to visit both. If I was more into zoos back then I'd probably have visited Taronga instead of these two, but it was definitely a fun day with two great, small parks.
Central Park Zoo + Prospect Park Zoo: Two first time visits to fairly small zoos that are very easily combined by public transport. On the same day I also birded in Central Park before, between and after these zoo visits, so it was definitely an easy combination!
Den Bla Planet + Copenhagen Zoo: Also two first time visits on the same day!
@Penshet and I arrived in the airport and planned to visit Den Bla Planet on the first day and Copenhagen Zoo on the next day, but we found ourselves having enough time to do both in one day quite comfortably! We did miss a few species and a well-hidden night house in Copenhagen Zoo though, so we visited that again on the next day.
Usti Zoo + Decin Zoo: Very much an impromptu visit to Decin together with
@KevinVar and
@GerbenElzinga turned our Usti-day into a two-day-visit day. A fairly comfortable combination which left enough time to see everything at both collections well (though we did manage to miss the serow!). Of course, now that Decin has two species of bird-of-paradise and Usti lost its serow that probably makes Decin the more attractive zoo to prioritize!
Singapore River Safari + Singapore Night Safari: A perfect combination that allows you to fill in the morning however you want, casually arrive and have plenty of time to see both zoos completely. If in a rush I'd say the two are also perfectly combineable with Singapore Zoo!
Duisburg Zoo + Krefeld Zoo: Probably the most rushed multiple-zoo day on this list! Definitely a good day, but only really possible because I didn't have many targets at Duisburg (I had been before and just wanted to see the river dolphin and king colobuses again) so I was able to go through the entire zoo very quickly, which left enough time for seeing everything in Krefeld twice. This combination would be a lot less comfortable now that Krefeld's bird house is open again, however!
The above were probably the only occasions where I've combined two "major" zoos together. Below is a list of other days where I've visited a larger collection together with a very closely located, usually very small collection.
Antwerp Zoo + Aquatopia
Poznan Nowe Zoo + Poznan Stare Zoo
Prague Zoo + Prague Sea World
Prague Zoo + Prague Crocodile Zoo
Plzen Zoo + Plzen AkvaTera
S.E.A. Aquarium + Sentosa Butterfly Park
El Nispero Zoo + Butterfly Haven + Serpentario El Valle