they affect two different mechanics.
spell hit counters resists which are level-bassed. these are "misses" where your spell does not hit the target. in pvp, you only need 3%. in pve, you need as much as 16% including talents.
spell penetration counters resistances to schools of magic (fire resistance for example). a spell can be resisted 0%, 25%, 50%, 75% or 100%. a 100% resist will look the same as a level-based resist.
in pvp, most people will have small amounts of resistances (pala aura is 60 to one school, mage armor is 18 to all, MotW is 25 to all). nowadays, most gear has no resistances at all, except full resist gear for some pve encounters which people will not wear in pvp because it gimps other stats too much.
conclusion:
in pve, most mobs have little to no school resistances. some have immunities, but these cannot be countered with spell penetration (like al'ar's fire immunity). in a raid you will have curse of elements/shadows which reduces resistances by 88! this is sufficient.
i do suggest getting 20 spell penetration enchanted on your cloak for a pve mage, as there is nothing else useful. -2% threat is crap, you have invisibility. apart from that, you can ignore spell penetration.
there's 20 spell penetration on the t4 robe, but i don't really know why.
in pvp, people have small resistances, but nothing to worry too much about. you could also get the 20 spell pene on your cloak.
Edited, Dec 19th 2007 11:39am by Turicus