As far as standard wild pets go, my favorites are Mirabilis, Ardur, Paor, Skaldyr, and Intes! I also have a soft spot for Zaphao and Malal. Basically all the hard-to-find standard eggs, haha!
Favorite holiday pets are Easero and Vaspi, with Ebilia, Uilus, Jaaku, Iluvu, and Divuin as close runners-up.
Favorite CS pets are Jahra, Noctis, and Aerix, with a soft spot for Drachid and Ezahni.
Favorite retired pets are Omni and Kioka. They're why I joined the site in the first place!
My favorite Uldavian pets are Galta and Cyancu. I'm so happy there was another Uldavian by the time I came back to the site. I still don't have either, though... Kir quests are hard.