Spell PenetrationFollow

spell penetration is to avoid partial resists like your SB does 2k damage and the opponent gets only hit by 1k damage and resists 1k, this is a really crude example but the more spell penetration you got the lower your partial resists will be.
Spell Penetration vs Stamnina, hmm hmm hif you focus more on pvp go for the stamina if you go pve go for the spell penetration if you got a socket "to spare" there is als an elixir(guardian) out there which lowers targets resistances which again helps to lower your partial resists. i think the elixir is called elixir of empowerment.

Spell penetration I think is most needed for boss fights, where bosses have high "resists" to spells, so to speak.

Sta and resilience are most needed for pvp/bg/arena.

I read a while ago on Wowiki that with CoS/CoE up and the spell penetration enchant on the cloak you should be fine in most pve cases, so if you mainly do PvE I would not recomend the spell penetration gem. However, I went looking for the page that I found this info off of and could not find it, so I may be wrong, but until I am told otherwise thats what I'm gunna stick with. And if your fighting something with alot more resistance thats where the elixers come in as Oaken mentioned.

With the exception of a handful of fights in Black Temple and a few trash mobs in Kara, no raiding-level content has resists. Bosses have an innate 26 (or 24? I can't remember) resist that cannot be gotten rid of my any means, so a grand total of ~6% of your damage is lost from partial resists that cant' be gotten rid of.

Spell penetration is a PvP stat and nothing more, and until you're well-geared usually isn't worth sacrificing health/resilience for. Get a Glowing Nightseye in the socket unless you're heavy in PvP, and then get the sta/res or stamina gem.