You may want to sit a moment and look over you collection. It is remarkable but yes, depending on what you want to do you may want to thin out your collection.
Are you collecting for collection/vanity pets sake? Then the normal criteria is any non-cageable or non-tradeable are to be "released" keeping rarest (blue) then keeping the highest level.
For example you have 3 Bandicoon pets. 1 is level 25 blue, level 21 blue & level 21 green. Of these 3 the level 25 would be the one to keep and release the other two.
If you are collecting for the sake of really putting some serious time & effort into both battling pets fights with npc's as well as with other players then you may want to see which pets have the best ratings/comments as to how they fair in fights.
For example (& for the sake of illustration) you have 5 Ghostly Skulls; 3 H/P & 2 H/B. since the H/P hits harder than the H/B cage those and then keep 2 because in some tournaments you will need them to get you thru without having to heal in between fights.
All pets are worthwhile & precious but definitely in the "eye of the beholder". Once you have determined what it is you plan to do then go from there. For those pets you can cage but only want 1 of them put them in a bank and then gauge if its worth selling or just saving for another time.
Hope this helps.