Similar in meaning:
* Murmured
* Mumbled
* Hushed
* Softly spoken
* Under one's breath
* In a low voice
More intense:
* Hissed
* Squealed
* Gasped
More formal:
* Uttered in a low tone
* Spoken confidentially
* Spoke in a hushed voice
Figurative:
* The wind whispered through the trees. (This suggests a gentle sound)
The best synonym will depend on the context of the sentence and the feeling you want to create.