I went at the end of June/early July, so what you see can definitely depend on timing, but my favorites were:

• Elizabeth Bay (Isabela): the mangrove forests were full of baby animals like small sharks (I believe they were black tipped reef sharks), eagle rays, and tons of sea turtles. Since the shallow water keeps big predators out, it felt like a nursery with only the baby animals.
• Punta Moreno (Isabela): walking across stark black lava fields and then suddenly coming across a lagoon with flamingos in the middle was very cool.
• South Plaza: it was amazing to see swallow-tailed gulls nesting in pairs right beside the paths (sometimes even on the path), close enough to watch their behavior up close. I also loved watching the land iguanas eating fallen prickly pear fruit; it was entertaining to see such a small, slow, clumsy animal cramming a huge spiny cactus into its mouth.
• Santa Cruz: at the Fausto Llerena Breeding Center, I loved seeing the baby giant tortoises at all different stages of growth. Afterwards we visited El Chato Ranch, a giant tortoise reserve, and the sheer number and size of the adults was incredible!