Roywyn

Almost all the partial (and even some total I think) resists you see on raid bosses - and any mob with a level higher than you, i.e. 71+ - are due to level difference, and cannot be overcome by anything at all.

In PvE, 99% of the mobs you face have zero resistances, making spell penetration useless against them.

Noticable exceptions:
Molten Giants/Destroyers and Golemagg - fire resistance
Azuregos - frost resistance
Chromatic and Nether Dragonkin (UBRS, Netherstorm, Nazan in Hellfire Ramparts) - resistance to many schools
Arcane Protectors - ~150 arcane resistance

That should be about it, correct me if I missed something.

All other mobs you face have zero resistances (some are immune and you just have to switch spells scholls / raid spots, but that's another matter), having CoS/CoE will only increase the damage done by 10-13% and have no other impact.
No resistance there, nothing that spell penetration will change. Except for eating up item budget.

Unless you want to gear only for farming Heroic Ramparts, just forget about spell penetration.