I just missed the Good Zoo near Wheeling, WVa. No real excuse; it hadn't struck me that they'd have one and the "What to do in Wheeling" pamphlet didn't mention it. It doesn't seem like a great loss, small and not particularly distinguished place but it's a zoo and I wish I'd known about it.
I also missed the Beardsley Zoo in Connecticut. I was on a minor league baseball trip with a very good and highly esteemed friend who is just not a zoo fan. She wanted to see a couple of ballparks where there wasn't any game that day--which was not a sacrifice as I'm also a ballpark fan--but the zoo was about to close when we finally got there. Again, not a "must see" zoo but it's a zoo.
I missed the Living Desert Museum in Palm Desert CA but that was because I was there in July and at the time it was not open during the summer; this is understandable as average daily high there is 106 F. I see it's now open early morning to late afternoon.
I spent some time trying to find the Walk In the Wild zoo in Spokane WA. Then I found out that my guidebook was out of date and the zoo had closed half a dozen years before.