D.B.
Hi A.. I'm going through the same thing right now. My daughter will be three at the end of February. Her magic hour is between 3 - 4 am. (Last night it was 4 and I am now exhausted this morning.) And who does she call out for? Mommmy, of course. Daddy meanwhile is sleeping soundly.
As tempting as it is to bring her into our bed, I am resisting that completely. I know her, it would start a habit that would be traumatic to break. So instead, I go to her bed. It seems like the lesser of two evils right now. I sleep with her until she falls back to sleep and then like a CIA spy, I slither out of the bed so as not to wake her and tiptoe across creaky hardwood floors back to my room. The worst is when she hears the hardwoods creaking (I swear this girl has mastered the art of being both completely asleep and completely awake at the same time!), wakes up and we start the process all over again.
I have turned the heat down really low at night to help her (all of us) sleep better. I think sometimes it helps, as some nights she actually will sleep all the way through. But apparently it's not the only answer, because it's not foolproof. I really think it's just another sleep phase that will work itself out. She understands fear now, and so instead of falling back asleep when she wakes up during the night, she starts to feel alone and afraid in the dark.
I usually give her a few minutes after she calls out, to see if she'll fall back asleep on her own -- and on occasion she does. It's like she's calling out in her sleep. But if her cry out gets louder and stronger and ends with "Mommy, I'm scared," then I'll go lie down with her until she falls back to sleep.
Hang in there.