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Spell penetration reduces the target's resistance to your spells; it is a different mechanic from spell hit rating. Spell penetration only works against targets with resistances, and will not reduce resistances below zero.
Spell penetration typically is a PvP stat, intended to help casters against players who wear resistance gear or are buffed with extra resistance, such as 
[Mark of the Wild]. In PvE, targets of a higher level than the caster have a base resistance (2% of mitigation per level difference) which cannot be overcome by spell penetration nor by any other stat. Otherwise, very few mobs and raid-level bosses have a substantial amount of resistance to overcome.
Formulas
The formula for spell penetration is quite simple. Each point of spell penetration negates one point of a target's resistance. Spell penetration cannot reduce a target's resistance below zero. The following equation gives effect of spell penetration on resistance, where P is the caster's spell penetration, and Rb is the target's base resistance. Here, the min() operator means the minimum of two values - in this case, it shows that spell penetration greater than a target's base resistance has no effect.
R = Rb - min(P, Rb)
For example, a level 70 player with 30 spell penetration casts a fire spell at another level 70 player buffed with 40 fire resistance. The spell resist check will be done as if the target only had 10 fire resistance. A level 70 player with 100 spell penetration casting at the same target will have his fire spell's resist check done as if the target had zero fire resistance (not -60).
For additional resistance due to level difference, spell penetration has no effect. In this equation, Lt is the target's level and Lc is the caster's level. For more details on this equation, see the resistance article.
R = Rb + min((Lt - Lc) * 5, 0) - min(P, Rb)
For example, A level 70 player casts a fire spell at a level 73 raid boss with no innate resistance. The level difference is 3, so the raid boss has effectively 15 resistance to all schools against the level 70 caster. No matter how much spell penetration the caster has, his spell's resist check will always be done as if the target had 15 resistance.
Increasing Spell Penetration
The following increase spell penetration:
- Mage:
[Arcane Subtlety] - Warlock: Curse of Shadows, Curse of Elements
- Spell penetration gear, gems and enchants
Talents such as the mage's 
[Elemental Precision], 
[Arcane Focus], the priest's 
[Shadow Focus], and the warlock's 
[Suppression] do not affect spell penetration. Those talents affect spell hit rating.
Using Spell Penetration
Especially in PvP, it is difficult to find a well-balanced amount of spell penetration. Against targets with no resistance, it has no effect (and as such is wasted). However, against targets with resistances, spell penetration is a powerful and, in terms of item values, cheap stat. Ideally, a caster should have exactly as much spell penetration as necessary to lower the target's resistance to zero.
In PvP, good spell penetration values are 40 (to counter [Mark of the Wild]) and 70 (to counter various single-school resistance buffs, such as the Paladin's resistance auras); these are usually enough. In PvE, where only few mobs have resistances, especially with 
[Curse of Shadow]/Elements active, spell penetration has not much use.
Spell penetration's effectivity increases with the target's resistances; i.e. reducing resistance from 100 to 80 results in a higher benefit than reducing it from 20 to 0. However, at some point it might be better to stick to another school, instead of stacking huge amounts of spell penetration at the cost of other stats.
See also
External links
- Reports of level-based resistances uncounterable by penetration gear.
- GLOCK: A mod which parses damage done to a mob to determine its base resistance.