I ran across this WarcraftPets forum post a while back: http://www.warcraftpets.com/community/forum/viewtopic.php?f=3&t=1620
. It lists the upgrades stones by family, in order of value. It's a subjective list but should help you think through what your priorities might be when using that flawless stone.
Personally, I can already agree on one count: the poster lists undead and elemental stones as the least valuable, and I tend to collect those stones before I have a strong candidate to use one. (By this reasoning, don't upgrade the unborn valk'yr -- if you do the trainer battles, you'll likely farm up a stone)
Whereas the stones that the poster listed as the most valuable, humanoid and magic, I have gotten few of (one each) and need badly.