Hi azcheetah2: if you needed to pick I would recommend Fresno as it is a larger zoo with more animals. I also love Micke Grove and it needs a lot of support. They have a great staff and were in the middle of building a new snow leopard-Asian small clawed otter complex when the horrible recession hit. They have lost staff positions and consequently their AZA accreditation. Hopefully that will turn around.
Fresno has a fairly comprehensive collection for its small size (Asian elephants, giraffes, orangutans, good reptile house, sea lions (new exhibit under construction), tigers, rain forest aviary, Malayan tapirs, peccaries, giant anteaters, among other species).
Sacramento has a zoo in a beautiful botanical setting. It also has a good collection for its size (giraffes, orangs, good reptile house, Coquerel's sifakas, Grevy's zebras, lions, tigers, jaguars, snow leopards, tamanduas, thick-billed parrots, yellow-billed magpies, red pandas, giant anteaters, chimpanzees).
Micke Grove has a nice lemur exhibit, a good puma exhibit, a good Mediterranean aviary with Waldrapp's ibis (or at least used to). They used to have Chinese alligator and Rodrigues fruit bats, but I think that these species have left.
I hope that you have a good trip. All three of these zoos are within 3 hours of each other on Highway 99 and could conceivably be visited on an ambitiously busy day.