Nothing in D&D 3.5 that I've found gives a creature more knowledge of spells it casts than what the Player's Handbook says a creature knows about the spells it casts.
What the Player's Handbook does not say is that a creature has special knowledge of a spell if the creature is that spell's caster. There's usually no indication to the caster—or anyone else—that a spell with no perceptible effect has run its course, been suppressed, or been dispelled. Trial and error and the ability to detect magical auras are the only actual indicators that such a spell's effect is ongoing.
A specific spell may indicate otherwise, of course—for example, the caster knows when a creature triggers her alarm spell, but absent a personal exception to the contrary a caster does not know when her alarm spell's been disabled, dispelled, or suppressed. Similarly, for example, this means that a caster usually doesn't know until it's too late that her protection from energy spell has been dispelled.
However, a DM should be cautious and consistent about this lest he alienate players. Explaining at a new campaign's start that this is how spells work in this campaign is much less stressful than trying to implement such rules in an ongoing campaign wherein the players had previously been given perfect knowledge of their spells!
In this DM's campaigns, a caster does have perfect knowledge of a spell's remaining duration if that duration is neither instantaneous nor permanent, this DM assuming that part of caster training is keeping such a precise mental stopwatch and saving this DM from having to do that bookkeeping.
