Kafi fur dich has a play area that has some books, toys, and even a giant chalk board with chalk. It's located in Kreis 4 on Stauffacherstrasse close to either Helvetiaplatz (tram 8 or bust 31) or Baeckeranlage (tram 8 or bus 31).
I go quite often with my 18month old daughter, and as long as she's not hitting some other kid, I can often sip my coffee in peace while she plays.
Dini Muetter on Langstrasse (next to the line 32 bus station Kernstrasse) has a big trunk of puzzles, books, and a few toys, but no designated play area...
The Migros Resturant next to Talwiesenstrasse (tram 9, and 14?) has a jungle gym type of play area.... not bad, and a LOT cleaner than McDonalds (I went there once and will never go back aaack.)
I hope that helps-- I'd also love to hear about any other places to go as well.
Ah- I forgot-- the restaurant/cafe at the park Baeckeranlage has a play area as well. It's not as nice or clean as some of the other places i mentioned, but you might want to give it a try.