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.
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.
Note that there is a +20 cap to bonuses to saving throws. Spellcraft, the champion of Torm's Sacred Defense, and any other saving throw bonuses (such as from spells or items) count toward the +20 cap (though spellcraft only counts towards saves versus spells while other bonuses may apply to all saves). Therefore, having more than 100 spellcraft is useless for the purpose of saves versus spells (since the bonus only goes up to +20) -- and less if they have other bonuses. For example, with 20 levels of champion of Torm (which gives +10 saves), anything over 50 spellcraft will not help.