I think that Gaeta's song was about the hybrid that had been unplugged. If you watch the episode, it was quite a coincidence that she was plugged in, woke up, and jumped while Gaeta is singing "to have her please just one day wake..."

Other parts of the song, that make me think hybrid--"avoid the dark and laughing rain"-- the sound of rounds of ammunition from Viper bullets hitting the baseship out in space?

As to what this means about Gaeta being a transsexual cylon, I hope not... But maybe he IS "Kat" reincarnate... they both annoy me, and they seemed like the same person :)