The PRD describes several types of saving throw, including "Negates" and "Disbelief":
Negates: The spell has no effect on a subject that makes a successful saving throw.
Disbelief: A successful save lets the subject ignore the spell's effect.
The only semantic difference between "you can ignore the spell effect" and "the spell has no effect on you" I can figure out is that the first one is voluntary (so you can choose not to disbelive). But the PRD says you actually can forego a saving throw (it includes the "Negates" type, doesn't it):
Voluntarily Giving up a Saving Throw: A creature can voluntarily forego a saving throw and willingly accept a spell's result.
I guess you "disbelieve" illusions and "negate" any other effects, but it is nothing but fluff. What is the mechanical difference between them?