On Fedora with Gnome-shell 3, its been long time that I was not able to get transparent window. So, finally I thought to spend some time to try to fix that. Finally got that fixed with all the configurations below in the conkyrc. Here the default color is set to LightSkyBlue but feel free to change that.
I hope this helps fedora community who is struggling to get transparent window. And here is the code :
own_window_transparent yes own_window_class Conky own_window_argb_visual yes own_window_argb_value 0 own_window_type normal own_window_colour LightSkyBlue own_window_hints undecorated,below,sticky,skip_taskbar,skip_pager