It honestly depends a lot on the pet and what you want to do with it.
Example 1: Fluxfire Feline can be breed 5 (pure Speed) or breed 8 (a split between Power and Speed), but most people consider breed 5 to be superior for Fluxfire because it has extremely low HP and cannot stand up well against enemy hits. Additionally, its attacks already hit hard enough that it doesn't really need more Power (it hits for nearly 2k even as breed 5). Breed 5 puts its Speed at level 25 at 325, which is higher than most epic Tamer pets and even some legendaries.
Example 2: Ghostly Skull can be breeds 6 (pure HP), 7 (split HP/Power), or 12 (HP and a balanced split), but I consider breed 7 to be the clear and easy winner for Ghostly Skull. The only gain for breed 12 over breed 6/7 is a tiny bit of speed but that still puts the Skull's speed at level 25 at an abysmal low number of 241. Literally almost every pet will be faster than a Skull regardless of breed, so there is zero point in wasting the extra bit on Speed. As for the debate between 6/7, I lean heavily in favor of breed 7. Ghostly Skull needs to have the highest Power possible because it will rely mostly on Ghostly Bite for damage, and you really want that ability to hit like a freight train. If you were building a Skull around Unholy Ascension for some reason (rather than Ghostly Bite), I'd agree breed 6 was a good choice too though.
Sometimes pure breeds (4, 5, and 6) are actually not desirable. For example, lots of flying-type pets have breed 5 (pure Speed), but this ultimately defeats the purpose of their flying passive. I really like the Wildhammer Gryphon Hatchling because it has a breed 4 (pure Power) option which lets it hit extremely hard while still going first for the first 50% of its HP.
Additionally, you generally do not want Speed breeds (5, 8, 9, 11) for pets with Surge or Charge or Rush. There are exceptions in cases where Surge is actually not the move you'd want to use on that pet, but that is the general rule.
Lastly (for now), you also have to consider attack multipliers. For example, Claw, Bite, etc all are "standard" attacks and scale 1:1 with Power, but moves like Haymaker scale 2.5:1 with Power and that makes Power extremely desirable for those types of pets.
Breed Resources: I highly recommend Warla's site (http://schaffhauser.me/Warcraft) for in-depth analysis of breeds + tons of pet information and the in-game addon Battle Pet BreedID (http://www.curse.com/addons/wow/battle_pet_breedid) for quick in-battle breed information.
Edited by Simca on 12/12/2012 4:52 PM PST