Check: A successful check means that your character has identified a spell being cast by an opponent. The difficulty class of this check is equal to 15 + spell level. The character also gains a +1 bonus for every 5 ranks in this skill to all saving throws against spells.
Special: A specialist wizard gets a +2 bonus when dealing with a spell from his specialized school. As well, a successful spellcraft check is required before your character can attempt to counterspell. The specialist wizard suffers a -5 penalty when dealing with a spell or effect from a prohibited school.
Use: Spellcraft checks are automatic whenever a spell is cast nearby.
Epic spells are automatically identified when they are cast; no spellcraft check is used for them.
The maximum useful spellcraft level for identifying spells is nominally 23 (as the maximum DC is 15 + 9 = 24), but it goes up to 28 if dealing with a prohibited school.
Unlike with other skills (such as the AC bonus from tumble), the saving throw bonus is based on fully modified ranks (not base ranks). Hence epic skill focus in spellcraft grants a +2 bonus to all saving throws against spells.
A negative spellcraft – such as when a curse song lowers your skills – will provide a penalty for saving throws against spells (-1 for each -5 points). However, since spellcraft requires training, the penalty will only occur if the player has at least one rank in spellcraft. For example, if a character who put no skill points into spellcraft is cursed for -6 points, they will receive no penalty, since they're not trained in spellcraft and can't use it. If a character that has 1 rank in the skill is cursed for -6 points, they will get -1 saves versus spells.
The maximum useful spellcraft level for saving throw bonuses is nominally 100, as the bonus counts toward the +20 cap on saving throw bonuses. (The maximum benefit may be achieved earlier if other bonuses apply.) However, this goes up to 105 if dealing with a prohibited school.