I don't believe we have a filter for that on WarcraftPets at the moment. If there is enough interest in seeing this filter added, perhaps it will go on the "to do" list for future website features/additions.
That being said, each pet profile does list the maximum number allowed in the Pet Journal. Example: Alliance Balloon
, Pet Journal Limit: 3 allowed
I think in general, you can safely include most achievement pets (Blue and Gold Mini-Jouster not included), Pet Store pets (excluding the Guardian Cub), and the Collector's Edition pets into the "1 allowed" category.