The majority of my pets have been given official nicknames, and it's mainly just the companions released in 5.1 that need new handles. I've only named about half and I'm already hitting a wall.
Some of my favorites so far:
Baneling - LandmineVenomoth is actually the name of a moth Pokemon. :x I couldn't help it! I was at a loss for names since there are only so many "mothy" names out there.
Cinder Kitten - Pyromanicat
Imperial Moth - Venomoth
Jade Tentacle - Whippit
Viscidus Globule - Croco Koosu
The Viscidus Globule gets a special name since it's reminiscent of the slime that used to think it was a crocolisk. It was during WotLK, I think, and hunters found that they could tame the named slime in Sholazar Basin. The poor thing was so confused but Blizzard set it straight shortly after they found out about the mix up. Koosu doesn't have an identity crisis anymore, but it was fun while it lasted. It's a shame that I never got around to taming one of my own on my hunter, so I guess having a minipet similarly named is the next best thing. ;)
For the Pandaren Spirits, I gave them names after the Captain Planet Planeteers lol. What better fit than those that channel each element? Now that I look at them, though, the names seem kind of odd and I don't think many will get the reference. I mean, even I had to look up Planeteers' names lol, and I chose them heh. I guess it will be sort of an inside joke?
I've hit a mental block on additional names for the rest of my collection, so it's probably time for a break and a breather. Maybe in the near future I'll finish up the list. At the very least, I'd like to have all of my non-wild pets renamed before 5.2. There are lots of new pets coming that if I fall behind on renaming them, I'll never be able to catch up!