Runes of Magic US / AU

Quoted from "effervescent;575733"

You want a low level holy pet egg. High level pet eggs are trash, regardless of aptitude, and rune pets are the worst in terms of overall stats.

What most do is get a level 1-2 holy pet egg (not rune pet) with a decent amount of apt (80+ is best, but can be hard to find. Be prepared to spend several million at least on a good egg). You can raise the apt by chain merging pets into the holy pet egg, and using golden eggs to trade for Awakening Potions from the pet hunter in Miller's Farm. Each potion converts 1,000 training points (which you get from merging) into 1 aptitude point.

You keep doing this until your pet is maxed out on apt (note, you can shorten the time it takes to do this by buying blue rune pet eggs with 90+ apt to merge). THEN you start leveling it. With max aptitude, the stat gain per level will be much greater than buying a level 30 pet egg with low apt.

Just to note, to get pets to a high level once their apt is maxed, it is extremely costly. You will want to hold off on leveling it too far until you have the money to spend on it. Pet egg merging alone can get you to ~level 30 though if you troll the AH constantly, which is cheaper than the grind from 30-40 or above.

There's a more descriptive guide in the guide forum (it's a sticky) that Vfwiffo wrote for people wanting to learn how to level pets -- it explains the chain merging process very well. You should check it out for more in-depth information on pets.