If you look at the breed guide's overview, you could see that the total amount of stats decreases, the more stats are present in a breed. Therefore "pure" breeds, especially H/H and P/P, are often the better choice than, say, P/B.
However, you always should look at the entire skillset, including pet type. A very interesting example is the jade oozeling:
- being magical, it can't take more than 40 (35) % of it's max HP in a hit. the higher the oozeling's max HP, the more damage it takes before triggering the ability.
- it has two dots that increase it's attacks damage (acidic goo, corrosion)
- it has a self-heal that scales with damage (absorb). the higher it's damage, the higher it's self heal.
i won't get into details of the other skills because these are the skills of interest here.
now, what can we conclude from this? to be optimal, we want a P/P oozeling. a H/H oozeling would take more damage in a bursty hit and heal less overall. we don't need to be very speedy, so S/S won't help much. clearly a high power breed is optimal here.
if you wish to determine ideal breeds, take the pet's skillset into account. sometimes, you want the highest power, but also whenever breed doesn't matter, high power is the way to go because it can make fights shorter. high health can be interesting in combination with stuff that scales with max HP, like the humanoid bonus or explode-like abilities. it is also great for outlasting strategies. Speed is the trickiest of all stats, because more than one speed point above the enemy is essentially wasted (but not always either

). Generally speaking, you want the highest speed with speed related skillsets, because the enemy might use spells that increases their relative speeds. Speed is also very interesting in combination with spells like burrow because you can use them to react to the enemy's two-round spells, negating them.
Another thing you'd like to look at is similar pets that share abilities. As an example, if you already have a S/S mongoose, then you might want a P/S mongoose pup for greater variety. Technically, you don't need every pet to be the ideal breed if you already have a good one with that skillset. Personally, I'm still going for perfection, but this is just a time consuming hobby of mine.

However, going for a little variety, like in my mongoose example, might still be a good idea. Who knows, maybe one breed might turn out very good and in that case i'd rather already have it in my book than having to go back and farm for it. But that's just personal preference too.
Edit:
Kpb321 wrote:That addon sounds interesting. What is its name and where can I download it?
Looks like he means PetJournal Enhancer. A great addon i highly reccomend too. You might want to take a look at the Addons section of the site.