There aren't really any unique critters that I want to use for battles so I've just been picking ones I like to upgrade with the stones. The only critter I've really gotten a lot of use from has been a Shimmershell Snail.
Mechanical - Mechanical Pandaren Dragonling Undead - worth saving for Scourged Whelpling otherwise Ghostly Skull Beast - Flayer Youngling (P/P) since they're hard to farm good rares. Aquatic - Wanderer's Hatchling or Jubling. Flying - Gilnean Raven
Edit: As to your original question, I'd consider stoning an Irradiated Roach. That's been the hardest for me to find so far (still only have an uncommon) and I've captured a rare Minfernal and rare Scourged Whelplings of both breeds... and Irradiated Roach is the only one I check for on multiple servers. Starting to really hate that little bugger and considering going back to Valley of the Four Winds to top off leveling pets that are close to 25 in hopes of getting another critter stone.
I just got a critter stone and I was considering my irradiated roach, egbert, or one of the other uncommon event pets (like winter reindeer). I already upgraded my wolpertinger. Though, now that I saw the pug, I'm considering that too. It's tough because I seem to have more critters than any other type of pet and I find I don't use them enough as it is.
Any other critter suggestions? Especially ones with unique skills sets?
I have now acquired a Humanoid and Dragonkin stone, so what pets do you guys think I should upgrade with those? I already have rare crimson/jade/golden hatchlings and rare kun-lai runts. I was thinking Harpy Youngling, Sporeling Sprout, or Flayer Youngling for Humanoid and Infinite Whelpling, Proto-Drake Whelpling, Red Dragonhawk Hatchling, or Spawn of Onyxia for Dragonkin.