I used to use an addon which the name of eludes me at the moment, that tracked estimated resistance of mobs. An average raid boss had something like 28 resist to each tree on average, as a base. I always felt spell penetration was worth having and using. In a situation where you have Curse of Elements (mage perspective) perhaps its not worth having.
I also found this thread interesting from the penetration wiki
http://forums.subcreation.net/viewtopic.php?t=482 which is discussion based on penetration not working againt pve mobs.
I never seek out spell penetration, if i get some, so be it.