From memory:
Caster Level determines what you roll to penetrate SR.
Caster Level is used for any mechanical portion of a spell that scales with caster level (IE- Caster level 5 fireball does 5d6 damage and has a range of 600 ft.)
Caster Level is used for determining whether or not you qualify for certain feats, like Item Creation.
There may be more, but thats all I recall at this moment.
Technik