Wow, this is an old thread. I only had Zoee and Taz.
So, none of mine really have middle names. I say Zoee's is Jayne, but I never really use it on her.
Here are their most commonly used nicknames.
Zoee - Zo dog
Taggart - Tagg-Tagg-Tiggity-Tagg (how is this a nickname when it's soo long)
Paizly - Paizly Poo, or just Poop
Jax - Jaxter, Maxter

And then I refer to them by species and gender. Boy Dog, Girl Dog, Boy Cat, Girl Cat.