Has anyone nailed down the origin of this term? My off-the-cuff guess is that it mimics the theme from The Twilight Zone.

Used how?  I’ve heard people make this noise, mostly as an exclamation (or imitating a train whistle), but I don’t think I could ascribe a consistent meaning to it.

The OED2 has

woo-woo
Imitative of the sound of wind.
1841 CARLYLE Misc. Ess., Baillie (1872) VI. 215 The ever~moaning..unsyllabled woo-woo of wind in empty churches!

I think the poster means woo-woo as meaning eerie, otherworldly, mysterious, etc.

“I tried reading that book, but it was a little too woo-woo for my taste.”

It’s also been used to mean steeped in New Age nonsense.  Used commonly on Randi’s site http://www.randi.org/site/

I made a half-hearted effort to track it down, but quickly ran into the problem of too many false positive hits.

I’m still meaning to make a concerted effort on the term.