For the most part they are species only fish, but in the tank I have at home I have a figure 8 puffer and some glass fish and they get along great. I was also looking at getting a couple of bumble bee gobies for the tank as well. It all depends on the fish and weather or not they feel comfortable. Be sure there are plenty of hiding spots and keep an eye out for nipping.
My puffer took ofer a corner of the tank that has a bunch of plants and cover, and he will chase anyone that goese near it. He doesn't nip at them, but just chases them out of his corner.
I love my puffer...so fun.