At least that's my guess.

She sleeps in the shirt of man... OK, shirt and man could have a few meanings, but she is basically being kept in her Box by three male cylons (Simon, Dural and Cavil).

My three wishes... could also be my wishes for Number Three.

Spared pain from a dark and laughing rain - being box has allowed her to escape (for now) the Cylon civil war.

That she may find love - the oracle told her she would find love when she held Hera.

Finally the request that she wake obviously refers to her being unboxed.

While I'll grant that this could have many interpetations, assuming that it even applies to something on the show, this explanatin seems to me the most likely to survive Occam's Razor.

The questions then become where did the song come from, and how did Gaeta learn it? The easiest answer would be that he's the final cylon.